|
Name |
Accession |
Description |
Interval |
E-value |
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
5-157 |
4.52e-77 |
|
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: 227.01 E-value: 4.52e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV 84
Cdd:cd06130 1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1091029196 85 VAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYR-YGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:cd06130 81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
5-163 |
3.62e-60 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 184.61 E-value: 3.62e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:COG0847 2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLpGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161
|
..
gi 1091029196 162 LK 163
Cdd:COG0847 162 LR 163
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
5-157 |
1.25e-44 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 149.55 E-value: 1.25e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDY-FSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLP 83
Cdd:PRK06195 3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196 84 VVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDayRYGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:PRK06195 83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFysnID--NARLNTVNNFLGYEFK-HHDALADAMACSNI 156
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
5-165 |
3.20e-35 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 121.25 E-value: 3.20e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:smart00479 2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 83 PVVAHN-AAFDMNVLHQSLKQLNIETPSMIYF-CSYQLAKRTI-DAYRYGLKHLMKHYKLDFHG-HHDALNDAKACAmit 158
Cdd:smart00479 82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNpGLPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158
|
....*..
gi 1091029196 159 fRLLKHY 165
Cdd:smart00479 159 -KLFKKL 164
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
6-155 |
1.65e-24 |
|
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: 93.57 E-value: 1.65e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFETA--NGKRTSICSVGMVKVVN--NEIVESFYTLVNPFD--YFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:pfam00929 1 VVIDLETTglDPEKDEIIEIAAVVIDGgeNEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPV-VAHNAAFDM-NVLHQSLKQLNIETPSMI-YFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGH-HDALNDAKAC 154
Cdd:pfam00929 81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYkELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160
|
.
gi 1091029196 155 A 155
Cdd:pfam00929 161 A 161
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
2-173 |
1.40e-16 |
|
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: 74.02 E-value: 1.40e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFET-ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:TIGR00573 6 LDTETTGDNETtGLYAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDAKA 153
Cdd:TIGR00573 86 RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEITNSHRalHGALADAFI 165
|
170 180
....*....|....*....|
gi 1091029196 154 CAMITFRLLKHYDNLQSMLQ 173
Cdd:TIGR00573 166 LAKLYLVMTGKQTKYGENEG 185
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
5-157 |
4.52e-77 |
|
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: 227.01 E-value: 4.52e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV 84
Cdd:cd06130 1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLV 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1091029196 85 VAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYR-YGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:cd06130 81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPnHKLNTVAEHLGIELN-HHDALEDARACAEI 153
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
5-163 |
3.62e-60 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 184.61 E-value: 3.62e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:COG0847 2 FVVLDTETTGLDPAkdRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGGA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:COG0847 82 VLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLpGLPSYSLDALCERLGIPFDERHRALADAEATAELFLAL 161
|
..
gi 1091029196 162 LK 163
Cdd:COG0847 162 LR 163
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
2-168 |
4.30e-48 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 154.53 E-value: 4.30e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFET--ANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:COG2176 7 DLTYVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLKQLNIEtPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMIT 158
Cdd:COG2176 87 GDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLpELKSYKLDTLAERLGIPLEDRHRALGDAEATAELF 165
|
170
....*....|
gi 1091029196 159 FRLLKHYDNL 168
Cdd:COG2176 166 LKLLEKLEEK 175
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
6-157 |
1.23e-44 |
|
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: 145.14 E-value: 1.23e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFET--ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:cd06127 1 VVFDTETtgLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196 83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKH--LMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:cd06127 81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGllLAERYGIPLEGAHRALADALATAEL 157
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
5-157 |
1.25e-44 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 149.55 E-value: 1.25e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDY-FSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLP 83
Cdd:PRK06195 3 FVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNL 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1091029196 84 VVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDayRYGLKHLMKHYKLDFHgHHDALNDAKACAMI 157
Cdd:PRK06195 83 VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFysnID--NARLNTVNNFLGYEFK-HHDALADAMACSNI 156
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
5-165 |
3.20e-35 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 121.25 E-value: 3.20e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:smart00479 2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 83 PVVAHN-AAFDMNVLHQSLKQLNIETPSMIYF-CSYQLAKRTI-DAYRYGLKHLMKHYKLDFHG-HHDALNDAKACAmit 158
Cdd:smart00479 82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLPViDTLKLARATNpGLPKYSLKKLAKRLLLEVIQrAHRALDDARATA--- 158
|
....*..
gi 1091029196 159 fRLLKHY 165
Cdd:smart00479 159 -KLFKKL 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
5-163 |
3.23e-27 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 107.23 E-value: 3.23e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:PRK00448 421 YVVFDVETTglSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAY-RYGLKHLMKHYKLDFHGHHDALNDAKACAMITFRL 161
Cdd:PRK00448 501 ILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELkSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKF 580
|
..
gi 1091029196 162 LK 163
Cdd:PRK00448 581 LK 582
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
6-155 |
1.65e-24 |
|
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: 93.57 E-value: 1.65e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFETA--NGKRTSICSVGMVKVVN--NEIVESFYTLVNPFD--YFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:pfam00929 1 VVIDLETTglDPEKDEIIEIAAVVIDGgeNEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPV-VAHNAAFDM-NVLHQSLKQLNIETPSMI-YFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGH-HDALNDAKAC 154
Cdd:pfam00929 81 RKGNLlVAHNASFDVgFLRYDDKRFLKKPMPKLNpVIDTLILDKATYkELPGRSLDALAEKLGLEHIGRaHRALDDARAT 160
|
.
gi 1091029196 155 A 155
Cdd:pfam00929 161 A 161
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
2-157 |
3.72e-24 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 95.09 E-value: 3.72e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFETANGK--RTSICSVGMVKVVNNEIVESFYTLVnpFDYFSQTNI-EVHGITPEDVNDAPSFEYVFPYMMQF 78
Cdd:PRK08517 67 DQVFCFVDIETNGSKpkKHQIIEIGAVKVKNGEIIDRFESFV--KAKEVPEYItELTGITYEDLENAPSLKEVLEEFRLF 144
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196 79 IGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKHLMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:PRK08517 145 LGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAYEI 223
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
2-163 |
5.42e-23 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 90.73 E-value: 5.42e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFETA--NGKRTSICSVGMVKVVNNEIV--ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQ 77
Cdd:PRK09145 28 PDEWVALDCETTglDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLA 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 78 FIGKLPVVAHNAAFDMNVLHQSLKQL--------NIETPSMIYFCSY-QLAKRTIDAYrygLKHLMKHYKLDFHGHHDAL 148
Cdd:PRK09145 108 FIGNRPLVGYYLEFDVAMLNRYVRPLlgiplpnpLIEVSALYYDKKErHLPDAYIDLR---FDAILKHLDLPVLGRHDAL 184
|
170
....*....|....*
gi 1091029196 149 NDAKACAMITFRLLK 163
Cdd:PRK09145 185 NDAIMAALIFLRLRK 199
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-174 |
4.73e-21 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 89.63 E-value: 4.73e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 1 MENAFIALDFET-----ANGKRtsICSVGMVKVVNNEIVESFYTLVNPfdyfsQTNI-----EVHGITPEDVNDAPSFEY 70
Cdd:PRK08074 1 MSKRFVVVDLETtgnspKKGDK--IIQIAAVVVEDGEILERFSSFVNP-----ERPIppfitELTGISEEMVKQAPLFED 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 71 VFPYMMQFIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAK---RTIDAYRygLKHLMKHYKLDFHGHHDA 147
Cdd:PRK08074 74 VAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARillPTAESYK--LRDLSEELGLEHDQPHRA 151
|
170 180 190
....*....|....*....|....*....|..
gi 1091029196 148 LNDAKACAMITFRLLKH-----YDNLQSMLQI 174
Cdd:PRK08074 152 DSDAEVTAELFLQLLNKlerlpLVTLQQLRRL 183
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
5-157 |
9.18e-21 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 87.18 E-value: 9.18e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKL 82
Cdd:PRK06807 10 YVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091029196 83 PVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI-DAYRYGLKHLMKHYKLDFHGhHDALNDAKACAMI 157
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMkHAPNHKLETLKRMLGIRLSS-HNAFDDCITCAAV 164
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
2-182 |
3.32e-19 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 81.80 E-value: 3.32e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFETA--NGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK06310 6 DTEFVCLDCETTglDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLP-VVAHNAAFDMNVLHQSLKQLNIETPSMIYFC--SYQLAKRTIDAYRYGLKHLMKHYKLDFHGHHDALNDAKACAM 156
Cdd:PRK06310 86 KEGDyIVGHSVGFDLQVLSQESERIGETFLSKHYYIidTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINIK 165
|
170 180
....*....|....*....|....*.
gi 1091029196 157 ITFRLLKHYDNLQSMLQIYGKNLKDK 182
Cdd:PRK06310 166 VFKHLCKRFRTLEQLKQILSKPIKMK 191
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
5-153 |
1.45e-18 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 82.27 E-value: 1.45e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRT--SICSVGMVKVVNNEIVESFYTLVNPfdyfsQTNIEVH-----GITPEDVNDAPSFEYVFPYMMQ 77
Cdd:PRK07883 17 FVVVDLETTGGSPAgdAITEIGAVKVRGGEVLGEFATLVNP-----GRPIPPFitvltGITTAMVAGAPPIEEVLPAFLE 91
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196 78 FIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTI---DAYRYGLKHLMKHYKLDFHGHHDALNDAKA 153
Cdd:PRK07883 92 FARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLprdEAPNVRLSTLARLFGATTTPTHRALDDARA 170
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
5-167 |
3.59e-18 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 77.59 E-value: 3.59e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFE-------TANGKRTSICSVGMVKV-VNNEIVESFYTLVNPfDYFSQTN---IEVHGITPEDVNDAPSFEYVFP 73
Cdd:COG5018 4 YLVIDLEatcwdgkPPPGFPMEIIEIGAVKVdENGEIIDEFSSFVKP-VRRPKLSpfcTELTGITQEDVDSAPSFAEAIE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 74 YMMQFIG-KLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSyqLAKRTIDAY----RYGLKHLMKHYKLDFHG-HHDA 147
Cdd:COG5018 83 DFKKWIGsEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRHIN--LKKLFALYFglkkRIGLKKALELLGLEFEGtHHRA 160
|
170 180
....*....|....*....|
gi 1091029196 148 LNDakacAMITFRLLKHYDN 167
Cdd:COG5018 161 LDD----ARNTAKLFKKILG 176
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
2-173 |
1.40e-16 |
|
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: 74.02 E-value: 1.40e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 2 ENAFIALDFET-ANGKRTSICSVGMVKVVNN-EIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:TIGR00573 6 LDTETTGDNETtGLYAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDAKA 153
Cdd:TIGR00573 86 RGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdttdTLQYARPEFPGKRNTLDALCKRYEITNSHRalHGALADAFI 165
|
170 180
....*....|....*....|
gi 1091029196 154 CAMITFRLLKHYDNLQSMLQ 173
Cdd:TIGR00573 166 LAKLYLVMTGKQTKYGENEG 185
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
5-164 |
1.78e-16 |
|
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: 73.02 E-value: 1.78e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTS-------ICSVGMVKVV--NNEIVESFYTLVNPFDYFSQTN--IEVHGITPEDVNDAPSFEYVFP 73
Cdd:cd06133 1 YLVIDFEATCWEGNSkpdypneIIEIGAVLVDvkTKEIIDTFSSYVKPVINPKLSDfcTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 74 YMMQFIGKLpvvaHNAAF------DMNVLHQSLKQLNIETPSMiYFCSY-----QLAKRTIDAYRYGLKHLMKHYKLDFH 142
Cdd:cd06133 81 EFLEWLGKN----GKYAFvtwgdwDLKDLLQNQCKYKIINLPP-FFRQWidlkkEFAKFYGLKKRTGLSKALEYLGLEFE 155
|
170 180
....*....|....*....|...
gi 1091029196 143 G-HHDALNDAKacamITFRLLKH 164
Cdd:cd06133 156 GrHHRGLDDAR----NIARILKR 174
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-163 |
2.33e-16 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 75.88 E-value: 2.33e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 1 MENAFIALDFE-TANGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK07246 5 KLRKYAVVDLEaTGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLkqlnietpsmiYFCSYQLAKRTIDAY-----------RYGLKHLMKHYKLDFHGHHDAL 148
Cdd:PRK07246 85 EDCIFVAHNVKFDANLLAEAL-----------FLEGYELRTPRVDTVelaqvffptleKYSLSHLSRELNIDLADAHTAI 153
|
170
....*....|....*
gi 1091029196 149 NDAKACAMITFRLLK 163
Cdd:PRK07246 154 ADARATAELFLKLLQ 168
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
6-152 |
2.69e-16 |
|
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: 72.18 E-value: 2.69e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFET-----ANGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:cd06131 2 IVLDTETtgldpREGHR--IIEIGCVELINRRLTgNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPsMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLD-----FHGhhdALND 150
Cdd:cd06131 80 RGAELVIHNASFDVGFLNAELSLLGLGKK-IIDFCrvidTLALARKKFPGKPNSLDALCKRFGIDnshrtLHG---ALLD 155
|
..
gi 1091029196 151 AK 152
Cdd:cd06131 156 AE 157
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
6-151 |
3.29e-16 |
|
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130473 [Multi-domain] Cd Length: 225 Bit Score: 73.20 E-value: 3.29e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFETANGKRTS---ICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGK 81
Cdd:TIGR01406 3 IILDTETTGLDPKGghrIVEIGAVELVNRMLTgDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFIGG 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1091029196 82 LPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSY----QLAKRTIDAYRYGLKHLMKHYKLDFHGH--HDALNDA 151
Cdd:TIGR01406 83 SELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVidtlAMARERFPGQRNSLDALCKRFKVDNSHRtlHGALLDA 158
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
5-181 |
7.18e-16 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 72.78 E-value: 7.18e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA-----NGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQF 78
Cdd:PRK07740 61 FVVFDLETTgfspqQGDE--ILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 79 IGKLPVVAHNAAFD---MN-VLHQSLKQ-LN---IETPSMIYFCSYQLAKRTIDAyryglkhLMKHYKLDFHGHHDALND 150
Cdd:PRK07740 139 IGAGVLVAHHAGHDkafLRhALWRTYRQpFThrlIDTMFLTKLLAHERDFPTLDD-------ALAYYGIPIPRRHHALGD 211
|
170 180 190
....*....|....*....|....*....|.
gi 1091029196 151 AKAcamiTFRLLKHYDNLQSMLQIYgkNLKD 181
Cdd:PRK07740 212 ALM----TAKLWAILLVEAQQRGIT--TLHD 236
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
9-157 |
3.85e-12 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 63.18 E-value: 3.85e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 9 DFETANGKRTS--ICSVGMVKV-VNNEIVESFYTLVNPFDYFSQTNIevHGITPEDVNDAPSFEYVFPYMMQFIGKLPVV 85
Cdd:PRK06063 21 DVETSGFRPGQarIISLAVLGLdADGNVEQSVVTLLNPGVDPGPTHV--HGLTAEMLEGQPQFADIAGEVAELLRGRTLV 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1091029196 86 AHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRT---IDAYRygLKHLMKHYKLDFHGHHDALNDAKACAMI 157
Cdd:PRK06063 99 AHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLglgLPNLR--LETLAAHWGVPQQRPHDALDDARVLAGI 171
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
6-160 |
4.90e-11 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.
Pssm-ID: 99847 Cd Length: 152 Bit Score: 57.91 E-value: 4.90e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFE---TANGKRTSICsvGMVKVVN---NEIVESFytlVNPF----DYfsqtNIEVHGITPEDVNDAPSFEYVFPYM 75
Cdd:cd06144 1 VALDCEmvgVGPDGSESAL--ARVSIVNedgNVVYDTY---VKPQepvtDY----RTAVSGIRPEHLKDAPDFEEVQKKV 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 76 MQFI-GKLpVVAHNaafdmnvLHQSLKQLNIETPS-MIY-FCSYQLAKRTIDAYRYGLKHLMKHY-KLDFH-GHHDALND 150
Cdd:cd06144 72 AELLkGRI-LVGHA-------LKNDLKVLKLDHPKkLIRdTSKYKPLRKTAKGKSPSLKKLAKQLlGLDIQeGEHSSVED 143
|
170
....*....|
gi 1091029196 151 AKAcAMITFR 160
Cdd:cd06144 144 ARA-AMRLYR 152
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
8-177 |
8.68e-11 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 58.58 E-value: 8.68e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 8 LDFETAnGKRTSICSVGMVKVVNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPymmQFIGKLPVVAH 87
Cdd:PRK07983 5 IDTETC-GLQGGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIP---HYYGSEWYVAH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 88 NAAFDMNVLhqslkqlnietPSMI--YFCSYQLAKRTIDAYRYGLKHLMKHYKLD------FHgHHDALNDakaCaMITF 159
Cdd:PRK07983 81 NASFDRRVL-----------PEMPgeWICTMKLARRLWPGIKYSNMALYKSRKLNvqtppgLH-HHRALYD---C-YITA 144
|
170 180
....*....|....*....|...
gi 1091029196 160 RLLKHYDNL-----QSMLQIYGK 177
Cdd:PRK07983 145 ALLIDIMNTsgwtaEEMADITGR 167
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
5-155 |
1.31e-10 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 58.40 E-value: 1.31e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETA--NGKRTSICSVGMVKVVNNEIV--ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVF-PYMMQFI 79
Cdd:PRK09146 49 FVALDFETTglDAEQDAIVSIGLVPFTLQRIRcrQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILdELLEALA 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 80 GKLPVVaHNAAFDMNVLHQSLKQL---NIETP---SMiyfcsyQLAKRTIDAYRYGL-KHLM-------------KHYKL 139
Cdd:PRK09146 129 GKVVVV-HYRRIERDFLDQALRNRigeGIEFPvidTM------EIEARIQRKQAGGLwNRLKgkkpesirladsrLRYGL 201
|
170
....*....|....*.
gi 1091029196 140 DFHGHHDALNDAKACA 155
Cdd:PRK09146 202 PAYSPHHALTDAIATA 217
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-151 |
2.97e-10 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 57.18 E-value: 2.97e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFET-----ANGKRtsICSVGMVKVVNNEIV-ESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFI 79
Cdd:PRK05711 7 IVLDTETtglnqREGHR--IIEIGAVELINRRLTgRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFI 84
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1091029196 80 GKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFC----SYQLAKRTIDAYRYGLKHLMKHYKLDfHGH---HDALNDA 151
Cdd:PRK05711 85 RGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCkvtdTLAMARRMFPGKRNSLDALCKRYGID-NSHrtlHGALLDA 162
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
5-157 |
4.14e-10 |
|
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: 55.90 E-value: 4.14e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 5 FIALDFETANGKRTS-ICSVGMVKVV--NNEIVESFYTLVNP-FDYFSQTNIEVHGIT----------PEDVN-DAPSFE 69
Cdd:pfam16473 2 HLMIDIETLGNEPTApIVSIGAVFFDpeTGELGKEFYARIDLeSSMSAGATIDADTILwwlkqssearAQLLGdDAPSLP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 70 YVFPYMMQFIGK------LPVVAHNAAFDMNVLHQSLKQLNIETPsMIYF--CSYqlakRTIDAYRYGLKHLMKHYKLDF 141
Cdd:pfam16473 82 DALLDLNDFIRDngdpksLKVWGNGASFDNVILRAAFERGGLPAP-WKYWndRDV----RTIVALGPELGYDPKRDIPFE 156
|
170
....*....|....*.
gi 1091029196 142 HGHHDALNDAKACAMI 157
Cdd:pfam16473 157 GVKHNALDDAIHQAKY 172
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
30-150 |
1.31e-09 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 55.20 E-value: 1.31e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 30 NNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYVFPYMMQFIGKLPV-VAHNA-AFDMNVLHQSLKQLNIET 107
Cdd:PRK06309 28 NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNIlVAHNNdAFDFPLLRKECRRHGLEP 107
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1091029196 108 PSMIYFCSYQLAKR-TIDAYRYGLKHLMKHYKLDFHGHHDALND 150
Cdd:PRK06309 108 PTLRTIDSLKWAQKyRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
6-171 |
4.51e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 51.13 E-value: 4.51e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 6 IALDFET--ANGKRTSICSVGMVKV-VNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDV--NDAPSFEyVFPYMMQFIG 80
Cdd:PRK07942 9 AAFDLETtgVDPETARIVTAALVVVdADGEVVESREWLADPGVEIPEEASAVHGITTEYAraHGRPAAE-VLAEIADALR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 81 KL-----PVVAHNAAFDMNVLHQSLKQLNIETP-SMIYFCSYQLaKRTIDAYRYG---LKHLMKHYKLDFHGHHDALNDA 151
Cdd:PRK07942 88 EAwargvPVVVFNAPYDLTVLDRELRRHGLPSLvPGPVIDPYVI-DKAVDRYRKGkrtLTALCEHYGVRLDNAHEATADA 166
|
170 180
....*....|....*....|
gi 1091029196 152 KACAMITFRLLKHYDNLQSM 171
Cdd:PRK07942 167 LAAARVAWALARRFPELAAL 186
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
1-173 |
1.12e-07 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 49.69 E-value: 1.12e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 1 MENAFIALDFE--------TANGKRTSICSVGMVKVVNNEIVESFYTLVNP--FDYFSQTNIEVHGITPEDVNDAPSFEy 70
Cdd:PRK07748 2 DEQQFLFLDFEftmpqhkkKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPktFPSLTERCKSFLGITQEDVDKGISFE- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 71 vfpymmQFIGKLPVVAH----------NAafDMNVLHQSLKQLNIETP--------SMIYfcsyqlaKRTI-DAYRYGLK 131
Cdd:PRK07748 81 ------ELVEKLAEYDKrckptivtwgNM--DMKVLKHNCEKAGVPFPfkgqcrdlSLEY-------KKFFgERNQTGLW 145
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1091029196 132 HLMKHYKLDFHG-HHDALNDakacAMITFRLLKHYDNLQSMLQ 173
Cdd:PRK07748 146 KAIEEYGKEGTGkHHCALDD----AMTTYNIFKLVEKDKEYLV 184
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
1-165 |
6.90e-07 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 48.13 E-value: 6.90e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 1 MENA--FIALDFET-----ANGKRTSICSVGMVKV--VNNEIVESFYTLVNPFDYFSQTNIEVHGITPEDVNDAPSFEYV 71
Cdd:PRK06722 1 MENAthFIVFDIERnfrpyKSEDPSEIVDIGAVKIeaSTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 72 FPYMMQFIGKLPVVAHNAAFDMNVLHQSLKQLNIETPSMIYFCSYQLAKRTIDAYRYGLKHL------MKHYKLDFHG-H 144
Cdd:PRK06722 81 IEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTpslqsaVEQLGLIWEGkQ 160
|
170 180
....*....|....*....|.
gi 1091029196 145 HDALNDAKACAMItfrLLKHY 165
Cdd:PRK06722 161 HRALADAENTANI---LLKAY 178
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
1-90 |
9.36e-06 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 44.00 E-value: 9.36e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1091029196 1 MEN--AFIALD--FETANGKrTSICSVGMVKVVNNEIVESFYTLVN---PFDYFSQTnieVHGITPEDVNDAPSFEYVFP 73
Cdd:PRK07247 1 MKRleTYIAFDleFNTVNGV-SHIIQVSAVKYDDHKEVDSFDSYVYtdvPLQSFING---LTGITADKIADAPKVEEVLA 76
|
90
....*....|....*..
gi 1091029196 74 YMMQFIGKLPVVAHNAA 90
Cdd:PRK07247 77 AFKEFVGELPLIGYNAQ 93
|
|
|