|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
32-206 |
7.84e-49 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 161.08 E-value: 7.84e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 32 NYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDnNKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREF 111
Cdd:COG2176 9 TYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVN-PG-RPIPPFITELTGITDEMVAD-APPFEEVLPEFLEF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTvLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKV 191
Cdd:COG2176 86 LGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAEL 164
|
170
....*....|....*
gi 489746013 192 FDEFHKLFKQEHMLR 206
Cdd:COG2176 165 FLKLLEKLEEKGITT 179
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
36-192 |
2.13e-41 |
|
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: 141.28 E-value: 2.13e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHG-EVVATFSELVKfPDNnKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREFIGS 114
Cdd:cd06127 3 FDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVN-PGR-PIPPEATAIHGITDEMLAD-APPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489746013 115 DPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDC-MHRMNIAENQEHRGLDDCLDTKKVF 192
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAELL 158
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
33-201 |
1.17e-31 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 124.95 E-value: 1.17e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 33 YTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPdNNKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREFI 112
Cdd:PRK00448 421 YVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIK-P-GHPLSAFTTELTGITDDMVKD-APSIEEVLPKFKEFC 497
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 113 GSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKVF 192
Cdd:PRK00448 498 GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLL 577
|
....*....
gi 489746013 193 DEFHKLFKQ 201
Cdd:PRK00448 578 IKFLKDLKE 586
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
36-192 |
2.04e-25 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 99.68 E-value: 2.04e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDnNKVPAFITKLNGIDEAAIeEKGLPVQEAIKKYREFI-GS 114
Cdd:smart00479 5 IDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVK-PD-RPITDYATEIHGITPEML-DDAPTFEEVLEELLEFLrGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 115 DPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYV-DVYRLARSFYPQERHNRLLDCMHRMNIAENQ-EHRGLDDCLDTKKVF 192
Cdd:smart00479 82 ILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARATAKLF 161
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
36-192 |
5.04e-22 |
|
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: 90.49 E-value: 5.04e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGE--VVATFSELVKFPDNNKVPAFITKLNGIDEAAIEEKGLpVQEAIKKYREFIG 113
Cdd:pfam00929 3 IDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPS-FEEVLEEFLEFLR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 114 SDPI-VGYNVNFDLNF-VYDLAE--KYHLTVLnNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQ-EHRGLDDCLDT 188
Cdd:pfam00929 82 KGNLlVAHNASFDVGFlRYDDKRflKKPMPKL-NPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGrAHRALDDARAT 160
|
....
gi 489746013 189 KKVF 192
Cdd:pfam00929 161 AKLF 164
|
|
| BRCT_DNA_ligase_like |
cd17748 |
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ... |
234-312 |
1.98e-12 |
|
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349379 [Multi-domain] Cd Length: 76 Bit Score: 61.73 E-value: 1.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 234 FIHKKVVIAGDLD-LDEYELANAVKNLGGFIQEEVGQDTDYVLVGDHDFFRtdvteLNKAKALKKQGQNIRTWSESFFLN 312
Cdd:cd17748 1 LAGKTFVFTGTLSsMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSK-----LKKGEELKAKGLGIKIISEEEFLD 75
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
31-192 |
1.32e-11 |
|
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: 63.24 E-value: 1.32e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 31 ENYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNnKVPAFITKLNGIDEAAIEEKGlPVQEAIKKYRE 110
Cdd:TIGR00573 7 DTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIK-PDR-PIDPDAIKIHGITDDMLKDKP-DFKEIAEDFAD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 111 FIGSDPIVGYNVNFDLNFV-YDLAEKYHLTVLNNDYVDVYRLARSFYPQ-ERHNRLLDCM---HRMNIAENQEHRGLDDC 185
Cdd:TIGR00573 84 YIRGAELVIHNASFDVGFLnYEFSKLYKVEPKTNDVIDTTDTLQYARPEfPGKRNTLDALckrYEITNSHRALHGALADA 163
|
....*..
gi 489746013 186 LDTKKVF 192
Cdd:TIGR00573 164 FILAKLY 170
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
32-206 |
7.84e-49 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 161.08 E-value: 7.84e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 32 NYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDnNKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREF 111
Cdd:COG2176 9 TYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVN-PG-RPIPPFITELTGITDEMVAD-APPFEEVLPEFLEF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTvLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKV 191
Cdd:COG2176 86 LGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAEL 164
|
170
....*....|....*
gi 489746013 192 FDEFHKLFKQEHMLR 206
Cdd:COG2176 165 FLKLLEKLEEKGITT 179
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
36-192 |
2.13e-41 |
|
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: 141.28 E-value: 2.13e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHG-EVVATFSELVKfPDNnKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREFIGS 114
Cdd:cd06127 3 FDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVN-PGR-PIPPEATAIHGITDEMLAD-APPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489746013 115 DPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDC-MHRMNIAENQEHRGLDDCLDTKKVF 192
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLlAERYGIPLEGAHRALADALATAELL 158
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
32-192 |
1.33e-38 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 134.15 E-value: 1.33e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 32 NYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNNkVPAFITKLNGIDEAAIEEKgLPVQEAIKKYREF 111
Cdd:COG0847 1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVN-PERP-IPPEATAIHGITDEDVADA-PPFAEVLPELLEF 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKV 191
Cdd:COG0847 78 LGGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAEL 157
|
.
gi 489746013 192 F 192
Cdd:COG0847 158 F 158
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
33-201 |
1.17e-31 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 124.95 E-value: 1.17e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 33 YTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPdNNKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREFI 112
Cdd:PRK00448 421 YVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIK-P-GHPLSAFTTELTGITDDMVKD-APSIEEVLPKFKEFC 497
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 113 GSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKVF 192
Cdd:PRK00448 498 GDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLL 577
|
....*....
gi 489746013 193 DEFHKLFKQ 201
Cdd:PRK00448 578 IKFLKDLKE 586
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
36-192 |
2.04e-25 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 99.68 E-value: 2.04e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDnNKVPAFITKLNGIDEAAIeEKGLPVQEAIKKYREFI-GS 114
Cdd:smart00479 5 IDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVK-PD-RPITDYATEIHGITPEML-DDAPTFEEVLEELLEFLrGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 115 DPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYV-DVYRLARSFYPQERHNRLLDCMHRMNIAENQ-EHRGLDDCLDTKKVF 192
Cdd:smart00479 82 ILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNPGLPKYSLKKLAKRLLLEVIQrAHRALDDARATAKLF 161
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
37-245 |
9.20e-24 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 101.53 E-value: 9.20e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 37 DVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVkfpdnN---KVPAFITKLNGIDEAAIEEKGlPVQEAIKKYREFIG 113
Cdd:PRK07883 21 DLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLV-----NpgrPIPPFITVLTGITTAMVAGAP-PIEEVLPAFLEFAR 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 114 SDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYP-QERHNRLLDCMHRM-NIAENQEHRGLDDCLDTKKV 191
Cdd:PRK07883 95 GAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPrDEAPNVRLSTLARLfGATTTPTHRALDDARATVDV 174
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 489746013 192 fdeFHKLFKQehmLRAQEaVKTL-DLTSEWPDIvkqtqafrSPFIHKKVVIAGDL 245
Cdd:PRK07883 175 ---LHGLIER---LGNLG-VHTLeELLTYLPRV--------TPAQRRKRHLADGL 214
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
28-195 |
2.48e-23 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 97.58 E-value: 2.48e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 28 GFPENYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNNkVPAFITKLNGIDEAAIEEKGLpVQEAIKK 107
Cdd:PRK06807 5 SLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVN-PERP-IPDRITSLTGITNYRVSDAPT-IEEVLPL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 108 YREFIGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYpQERHNRLLDCMHRM-NIAENQeHRGLDDCL 186
Cdd:PRK06807 82 FLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYM-KHAPNHKLETLKRMlGIRLSS-HNAFDDCI 159
|
....*....
gi 489746013 187 DTKKVFDEF 195
Cdd:PRK06807 160 TCAAVYQKC 168
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
36-192 |
5.04e-22 |
|
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: 90.49 E-value: 5.04e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGE--VVATFSELVKFPDNNKVPAFITKLNGIDEAAIEEKGLpVQEAIKKYREFIG 113
Cdd:pfam00929 3 IDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPS-FEEVLEEFLEFLR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 114 SDPI-VGYNVNFDLNF-VYDLAE--KYHLTVLnNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQ-EHRGLDDCLDT 188
Cdd:pfam00929 82 KGNLlVAHNASFDVGFlRYDDKRflKKPMPKL-NPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGrAHRALDDARAT 160
|
....
gi 489746013 189 KKVF 192
Cdd:pfam00929 161 AKLF 164
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
16-194 |
1.17e-19 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 86.61 E-value: 1.17e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 16 QDKIRQKGIEKPGFPENYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKFPDnnkVPAFITKLNGIdeAAIE 95
Cdd:PRK08517 53 ENLITLKTRFTPIKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKE---VPEYITELTGI--TYED 127
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 96 EKGLPVQ-EAIKKYREFIGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERH-----NRLLdcmh 169
Cdd:PRK08517 128 LENAPSLkEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYglsflKELL---- 203
|
170 180
....*....|....*....|....*
gi 489746013 170 rmNIAENQEHRGLDDCLDTKKVFDE 194
Cdd:PRK08517 204 --GIEIEVHHRAYADALAAYEIFKI 226
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
33-239 |
2.33e-17 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 82.69 E-value: 2.33e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 33 YTLIDVETTGLSPYR-DRITEMGGLKVRHGEVVATFSELVKfPdNNKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREF 111
Cdd:PRK08074 5 FVVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSFVN-P-ERPIPPFITELTGISEEMVKQ-APLFEDVAPEIVEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKV 191
Cdd:PRK08074 82 LEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTAEL 161
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 489746013 192 FDEF-HKLfKQ------EHMLRAQEAvktldLTSEWPDIVkqtqafrSPFIHKKV 239
Cdd:PRK08074 162 FLQLlNKL-ERlplvtlQQLRRLSDH-----LKSDIAELL-------DENILKKM 203
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
33-184 |
6.36e-16 |
|
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: 73.70 E-value: 6.36e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 33 YTLIDVETTglSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNNKVPAFItKLNGIDEAAIEEKGlPVQEAIKKYREFI 112
Cdd:cd06130 1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIR-PPTRFDPFNI-AIHGITPEDVADAP-TFPEVWPEIKPFL 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489746013 113 GSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIaENQEHRGLDD 184
Cdd:cd06130 76 GGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGI-ELNHHDALED 146
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
34-201 |
3.82e-14 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 70.85 E-value: 3.82e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 34 TLIDVETTGLSPYR-DRITEMGGLKVRHGEVVA-TFSELVKfPDNnKVPAFITKLNGIDEAAIEEkGLPVQEAIKKYREF 111
Cdd:PRK07740 62 VVFDLETTGFSPQQgDEILSIGAVKTKGGEVETdTFYSLVK-PKR-PIPEHILELTGITAEDVAF-APPLAEVLHRFYAF 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTKKV 191
Cdd:PRK07740 139 IGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKL 218
|
170
....*....|
gi 489746013 192 FDEFHKLFKQ 201
Cdd:PRK07740 219 WAILLVEAQQ 228
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
33-200 |
1.41e-13 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 69.09 E-value: 1.41e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 33 YTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNNkVPAFITKLNGIDEAAIEEKGlPVQEAIKKYREFI 112
Cdd:PRK06310 9 FVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLIN-PERV-VSAESQRIHHISDAMLRDKP-KIAEVFPQIKGFF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 113 GS-DPIVGYNVNFDLNFVYDLAEKYHLTVLNNDY--VDVYRLARsFYPQERHNRLLDCMHRMNIAENQEHRGLDDCLDTK 189
Cdd:PRK06310 86 KEgDYIVGHSVGFDLQVLSQESERIGETFLSKHYyiIDTLRLAK-EYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINI 164
|
170
....*....|.
gi 489746013 190 KVFDEFHKLFK 200
Cdd:PRK06310 165 KVFKHLCKRFR 175
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
32-313 |
2.21e-13 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 69.42 E-value: 2.21e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 32 NYTLIDVETTglSPYRDRITEMGGLKVRHGEVVATFSELVKFPDNNKVPAFItKLNGIDEAAIEEKgLPVQEAIKKYREF 111
Cdd:PRK06195 2 NFVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINI-GIHGIRPHMVEDE-LEFDKIWEKIKHY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 112 IGSDPIVGYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNIaENQEHRGLDDCLDTKKV 191
Cdd:PRK06195 78 FNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGY-EFKHHDALADAMACSNI 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 192 FDEFHKLFKQEHMlraQEAVKTLDLT----SEW---PDIVKQTQAFRS------------------PFIHKKVVIAGDLD 246
Cdd:PRK06195 157 LLNISKELNSKDI---NEISKLLGVTlgyvNENgykPSSRKGRILKRSnrqaprkkkkiiesfgftAFKEEVVVFTGGLA 233
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489746013 247 -LDEYELANAVKNLGGFIQEEVGQDTDYVLVGDHDFFRTDVTE----LNKAKALKKQGQNIRTWSESFFLNV 313
Cdd:PRK06195 234 sMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEmsnkLKKAIDLKKKGQNIKFLNEEEFLQK 305
|
|
| BRCT_DNA_ligase_like |
cd17748 |
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ... |
234-312 |
1.98e-12 |
|
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349379 [Multi-domain] Cd Length: 76 Bit Score: 61.73 E-value: 1.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 234 FIHKKVVIAGDLD-LDEYELANAVKNLGGFIQEEVGQDTDYVLVGDHDFFRtdvteLNKAKALKKQGQNIRTWSESFFLN 312
Cdd:cd17748 1 LAGKTFVFTGTLSsMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSK-----LKKGEELKAKGLGIKIISEEEFLD 75
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
31-192 |
1.32e-11 |
|
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: 63.24 E-value: 1.32e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 31 ENYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVATFSELVKfPDNnKVPAFITKLNGIDEAAIEEKGlPVQEAIKKYRE 110
Cdd:TIGR00573 7 DTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIK-PDR-PIDPDAIKIHGITDDMLKDKP-DFKEIAEDFAD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 111 FIGSDPIVGYNVNFDLNFV-YDLAEKYHLTVLNNDYVDVYRLARSFYPQ-ERHNRLLDCM---HRMNIAENQEHRGLDDC 185
Cdd:TIGR00573 84 YIRGAELVIHNASFDVGFLnYEFSKLYKVEPKTNDVIDTTDTLQYARPEfPGKRNTLDALckrYEITNSHRALHGALADA 163
|
....*..
gi 489746013 186 LDTKKVF 192
Cdd:TIGR00573 164 FILAKLY 170
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
27-166 |
1.85e-11 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 62.23 E-value: 1.85e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 27 PGFPENYTLIDVETTGLSPYRDRITEMGGLKVRHGEVVA--TFSELVKFPDNnkVPAFITKLNGIDEAAIEEkGLPVQEA 104
Cdd:PRK09145 25 PPPPDEWVALDCETTGLDPRRAEIVSIAAVKIRGNRILTseRLELLVRPPQS--LSAESIKIHRLRHQDLED-GLSEEEA 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489746013 105 IKKYREFIGSDPIVGYNVNFDLNFVyDLAEKYHL-TVLNNDYVDVYRLarsfYPQERHNRLLD 166
Cdd:PRK09145 102 LRQLLAFIGNRPLVGYYLEFDVAML-NRYVRPLLgIPLPNPLIEVSAL----YYDKKERHLPD 159
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
37-192 |
3.47e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 62.14 E-value: 3.47e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 37 DVETTGLSPYRDRITEMGGLKVRHGEvvaTFSELV--KFPdnnkVPAFITKLNGIDEAAIEEKGlPVQEAIKKYREFIGS 114
Cdd:PRK06309 8 DTETTGTQIDKDRIIEIAAYNGVTSE---SFQTLVnpEIP----IPAEASKIHGITTDEVADAP-KFPEAYQKFIEFCGT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 115 DPIV--GYNVNFDLNFVYDLAEKYHLTVLNNDYVDVYRLARSFYPQ-ERHNrlLDCMHRM-NIAENQEHRGLDDCLDTKK 190
Cdd:PRK06309 80 DNILvaHNNDAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDlPKHN--LQYLRQVyGFEENQAHRALDDVITLHR 157
|
..
gi 489746013 191 VF 192
Cdd:PRK06309 158 VF 159
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
32-192 |
4.46e-11 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 60.64 E-value: 4.46e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 32 NYTLIDVETTGLSPYRDR-----ITEMGGLKV-RHGEVVATFSELVKFPDNNKVPAFITKLNGIDEAAIEeKGLPVQEAI 105
Cdd:COG5018 3 KYLVIDLEATCWDGKPPPgfpmeIIEIGAVKVdENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVD-SAPSFAEAI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 106 KKYREFIGSDPIV----GynvNFDLN-FVYDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNRLLDCMHRMNI-AENQEH 179
Cdd:COG5018 82 EDFKKWIGSEDYIlcswG---DYDRKqLERNCRFHGVPYPFGDRHINLKKLFALYFGLKKRIGLKKALELLGLeFEGTHH 158
|
170
....*....|...
gi 489746013 180 RGLDDCLDTKKVF 192
Cdd:COG5018 159 RALDDARNTAKLF 171
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
37-182 |
6.78e-08 |
|
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99835 [Multi-domain] Cd Length: 167 Bit Score: 51.38 E-value: 6.78e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 37 DVETTGLSPYR-DRITEMGGLKVRHGEVVA-TFSELVKfPdNNKVPAFITKLNGIDEAAIEEKglPV-QEAIKKYREFIG 113
Cdd:cd06131 5 DTETTGLDPREgHRIIEIGCVELINRRLTGnTFHVYIN-P-ERDIPEEAFKVHGITDEFLADK--PKfAEIADEFLDFIR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489746013 114 SDPIVGYNVNFDLNFV---YDLAEKYHLTVLNNDYVDVYRLARSFYPQERHNrlLD-CMHRMNIaeNQEHRGL 182
Cdd:cd06131 81 GAELVIHNASFDVGFLnaeLSLLGLGKKIIDFCRVIDTLALARKKFPGKPNS--LDaLCKRFGI--DNSHRTL 149
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
27-129 |
1.56e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 51.90 E-value: 1.56e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 27 PGFPENYTLIDVETTGLSPYRDRITEMGGLKVRH------GEVVATFSELVKfPdNNKVPAFITKLNGIDEAAIEEKGLP 100
Cdd:PRK09182 33 GEFVRLGVILDTETTGLDPRKDEIIEIGMVAFEYdddgriGDVLDTFGGLQQ-P-SRPIPPEITRLTGITDEMVAGQTID 110
|
90 100 110
....*....|....*....|....*....|
gi 489746013 101 VQEAikkyREFIG-SDPIVGYNVNFDLNFV 129
Cdd:PRK09182 111 PAAV----DALIApADLIIAHNAGFDRPFL 136
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
36-192 |
1.78e-07 |
|
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: 50.30 E-value: 1.78e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDR-----ITEMGGLKV--RHGEVVATFSELVKFPDNNKVPAFITKLNGIDEAAIeEKGLPVQEAIKKY 108
Cdd:cd06133 4 IDFEATCWEGNSKPdypneIIEIGAVLVdvKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDV-DNAPSFPEVLKEF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 109 REFIGSDPIVGY--NVNFDLNFVYDLAEKYHLTVLN---NDYVDVYRLARSFYPQERHNRLLDCMHRMNIA-ENQEHRGL 182
Cdd:cd06133 83 LEWLGKNGKYAFvtWGDWDLKDLLQNQCKYKIINLPpffRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEfEGRHHRGL 162
|
170
....*....|
gi 489746013 183 DDCLDTKKVF 192
Cdd:cd06133 163 DDARNIARIL 172
|
|
| ExoI_N |
cd06138 |
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ... |
37-157 |
7.04e-06 |
|
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: 45.72 E-value: 7.04e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 37 DVETTGLSPYRDRITEMGGLKVRHgevvaTFSELVKF-----PDNNKVP---AFITklNGIDEAAIEEKGLPVQEAIKKY 108
Cdd:cd06138 4 DYETFGLNPSFDQILQFAAIRTDE-----NFNEIEPFnifcrLPPDVLPspeALIV--TGITPQQLLKEGLSEYEFIAKI 76
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489746013 109 REFIGSDP--IVGYN-VNFDLNFV----Y-DLAEKYHLTVLNN----DYVDVYRLARSFYP 157
Cdd:cd06138 77 HRLFNTPGtcIVGYNnIRFDDEFLrfafYrNLYDPYTWEWKNGnsrwDLLDVVRAYYALRP 137
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
36-129 |
1.72e-05 |
|
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. 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. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Pssm-ID: 99837 [Multi-domain] Cd Length: 189 Bit Score: 44.59 E-value: 1.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGE-----VVATFSELVK-FPDNNKVPAFItKLNGID------EAAIEEKGL---- 99
Cdd:cd06134 10 VDVETGGFNPQTDALLEIAAVTLEMDEqgnlyPDETFHFHILpFEGANLDPAAL-EFNGIDpfhpfrFAVDEKEALkeif 88
|
90 100 110
....*....|....*....|....*....|....
gi 489746013 100 -PVQEAIKKY---REFIgsdpiVGYNVNFDLNFV 129
Cdd:cd06134 89 kPIRKALKAQgctRAIL-----VGHNAHFDLGFL 117
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
29-71 |
2.79e-04 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 42.00 E-value: 2.79e-04
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 489746013 29 FPENYTLIDVETTGLSPYRDRITEMGGLKVR-HGEVVATFSELV 71
Cdd:PRK06063 13 YPRGWAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLL 56
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
50-213 |
1.89e-03 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 38.61 E-value: 1.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 50 ITEMGGLKVRHGEVVATFSELVkfpdNNKVP--AFITKLNGIDEAAIEeKGLPVQEAIKKYREFIGSDPIVGYNV-NFDL 126
Cdd:PRK07247 23 IIQVSAVKYDDHKEVDSFDSYV----YTDVPlqSFINGLTGITADKIA-DAPKVEEVLAAFKEFVGELPLIGYNAqKSDL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 127 NFV----YDLAEKYHltvlnndyVDVYRLARsfypqERHNRLLDCMHRMNIA--------ENQEHRGLDDCLDTKKVFDE 194
Cdd:PRK07247 98 PILaengLDLSDQYQ--------VDLYDEAF-----ERRSSDLNGIANLKLQtvadflgiKGRGHNSLEDARMTARVYES 164
|
170
....*....|....*....
gi 489746013 195 FHKLFKQEHMLRAQEAVKT 213
Cdd:PRK07247 165 FLESDQNKEYLEQQEEVTS 183
|
|
| Orn |
cd06135 |
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ... |
36-184 |
1.96e-03 |
|
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: 38.30 E-value: 1.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLkVRHGE--VVATFSELVKFPDNNkvpafitKLNGIDEAAIE------------EKGLPV 101
Cdd:cd06135 4 IDLEMTGLDPEKDRILEIACI-ITDGDlnIIAEGPELVIHQPDE-------VLDGMDEWCTEmhtksgltervrASTVTL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 102 QEAIKKYREFI------GSDPIVGYNVNFDLNFV----YDLAEKYHltvlnndyvdvYR---------LARSFYPQerhn 162
Cdd:cd06135 76 AQAEAELLEFIkkyvpkGKSPLAGNSVHQDRRFLdkymPELEEYLH-----------YRildvssikeLARRWYPE---- 140
|
170 180
....*....|....*....|..
gi 489746013 163 rlldcMHRMNIAENQEHRGLDD 184
Cdd:cd06135 141 -----IYRKAPKKKGTHRALDD 157
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
30-167 |
2.20e-03 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 38.39 E-value: 2.20e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 30 PENYTLIDVETTGLSPYRDRITEMG-GLKVRHGEVVATFselvkfpdnnkvpaFITKLNgiDEAAIEEKglpVQEAIKKY 108
Cdd:COG3359 14 SEDLLFFDIETTGLSGGGTVIFLIGlADGEGDGFVVRQY--------------FGEDPG--EEAALLEA---FLEWLADY 74
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489746013 109 refigsDPIVGYN-VNFDLNFVYDLAEKYHLTVLNNDY--VDVYRLARSFYPqerhNRLLDC 167
Cdd:COG3359 75 ------KLLVTYNgKSFDLPFLKTRFTLHRLPPPLPEFphLDLLHPARRLWK----NRLPSG 126
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
36-154 |
3.02e-03 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 37.58 E-value: 3.02e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489746013 36 IDVETTGLSPYRDRITEMGGLKVRHGEVVATfselvkfpdnnkVPAFITKLNgiDEAAIEEkglpVQEAIKKYRefigsd 115
Cdd:pfam13482 3 FDIETTGLSPGKNTIYLIGVYDVDGDKVRTF------------VQYLAEGPT--EEAAILQ----LFELLADYP------ 58
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 489746013 116 PIVGYNVN-FDLNFVYDLAEKYHLTVLNNdYVDVYRLARS 154
Cdd:pfam13482 59 LLVTFNGKsFDVPFIKRRFKRYDLDELFR-HIDLLHPLRK 97
|
|
| BRCT_RFC1 |
cd17752 |
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ... |
237-296 |
5.60e-03 |
|
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.
Pssm-ID: 349383 [Multi-domain] Cd Length: 79 Bit Score: 35.27 E-value: 5.60e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489746013 237 KKVVIAGDLD-LDEYELANAVKNLGGFIQEEVGQDTDYVLVGDHdffrTDVTELNKAKALK 296
Cdd:cd17752 9 LTFVITGVLEsLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRD----AGPSKLEKAKELG 65
|
|
| |
