|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-242 |
1.03e-157 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 436.98 E-value: 1.03e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 1 MRSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 81 IRGAQLIIHNAAFDIGFINNEFALLGqQDRSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDA 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLG-RDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 161 EILADVYLAMTGGQTSLSLAGSGAEGDGSGrpmVSPIRRLDPARVATPVLRANAEELAAHAARLAVIEKSaGGPSLWAQL 240
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLGFAMEGETQQQQG---EETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKK-GGSCLWRKY 238
|
..
gi 15597013 241 EA 242
Cdd:PRK05711 239 AE 240
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-231 |
6.18e-108 |
|
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: 310.48 E-value: 6.18e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 2 RSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFI 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 82 RGAQLIIHNAAFDIGFINNEFALLGQQDRsDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDAE 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIK-KIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597013 162 ILADVYLAMTGGQTSL-SLAGSgaEGDGSGRPMVSPIRRldpARVATPVLRANAEELAAHAARLAVIEKSA 231
Cdd:TIGR01406 160 LLAEVYLALTGGQESLlELAES--NSGEAAKPSKSAEMK---LGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
4-171 |
1.19e-106 |
|
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: 304.84 E-value: 1.19e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:cd06131 2 IVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGqqDRSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDAEIL 163
Cdd:cd06131 82 AELVIHNASFDVGFLNAELSLLG--LGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELL 159
|
....*...
gi 15597013 164 ADVYLAMT 171
Cdd:cd06131 160 AEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
4-172 |
1.19e-67 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 206.18 E-value: 1.19e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRLTgRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:COG0847 3 VVLDTETTGLDP-AKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGQQDRsdvteYCSVLDTLLMARERHPG-QRNNLDALCKRYGVDNSGRdlHGALLDAEI 162
Cdd:COG0847 81 AVLVAHNAAFDLGFLNAELRRAGLPLP-----PFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAEA 153
|
170
....*....|
gi 15597013 163 LADVYLAMTG 172
Cdd:COG0847 154 TAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
4-172 |
1.99e-50 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 162.47 E-value: 1.99e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRlTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:smart00479 3 VVIDCETTGLDP-GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHN-AAFDIGFINNEFALLGQQDRSDvteyCSVLDTLLMARERHPG-QRNNLDALCKRYGVDNSGRdLHGALLDAE 161
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGIKQPPK----LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155
|
170
....*....|.
gi 15597013 162 ILADVYLAMTG 172
Cdd:smart00479 156 ATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-167 |
1.63e-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: 1.63e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRL-TGRHFHVYLQPDR--EVDEGAIAVHGITNEYLKDKPRFREVANDFFEF 80
Cdd:pfam00929 1 VVIDLETTGLDP-EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 81 IR-GAQLIIHNAAFDIGFINNEFALLGQqdrSDVTEYCSVLDTLLMARERHPGQRNN-LDALCKRYGVDNSGRdLHGALL 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLK---KPMPKLNPVIDTLILDKATYKELPGRsLDALAEKLGLEHIGR-AHRALD 155
|
....*....
gi 15597013 159 DAEILADVY 167
Cdd:pfam00929 156 DARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-242 |
1.03e-157 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 436.98 E-value: 1.03e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 1 MRSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 81 IRGAQLIIHNAAFDIGFINNEFALLGqQDRSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDA 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLG-RDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 161 EILADVYLAMTGGQTSLSLAGSGAEGDGSGrpmVSPIRRLDPARVATPVLRANAEELAAHAARLAVIEKSaGGPSLWAQL 240
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLGFAMEGETQQQQG---EETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKK-GGSCLWRKY 238
|
..
gi 15597013 241 EA 242
Cdd:PRK05711 239 AE 240
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-231 |
6.18e-108 |
|
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: 310.48 E-value: 6.18e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 2 RSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFI 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 82 RGAQLIIHNAAFDIGFINNEFALLGQQDRsDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDAE 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIK-KIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15597013 162 ILADVYLAMTGGQTSL-SLAGSgaEGDGSGRPMVSPIRRldpARVATPVLRANAEELAAHAARLAVIEKSA 231
Cdd:TIGR01406 160 LLAEVYLALTGGQESLlELAES--NSGEAAKPSKSAEMK---LGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
4-171 |
1.19e-106 |
|
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: 304.84 E-value: 1.19e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:cd06131 2 IVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGqqDRSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHGALLDAEIL 163
Cdd:cd06131 82 AELVIHNASFDVGFLNAELSLLG--LGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELL 159
|
....*...
gi 15597013 164 ADVYLAMT 171
Cdd:cd06131 160 AEVYLELT 167
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
2-220 |
2.71e-70 |
|
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: 214.62 E-value: 2.71e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 2 RSVVLDTETTGM----PVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDF 77
Cdd:TIGR00573 2 RQLVLDTETTGDnettGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 78 FEFIRGAQLIIHNAAFDIGFINNEFALL--GQQDRSDVteyCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRDLHG 155
Cdd:TIGR00573 82 ADYIRGAELVIHNASFDVGFLNYEFSKLykVEPKTNDV---IDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHG 158
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15597013 156 ALLDAEILADVYLAMTGGQTSL-SLAGSGAEGDGSGRPMVSPIRRLDparvatpVLRANAEELAAH 220
Cdd:TIGR00573 159 ALADAFILAKLYLVMTGKQTKYgENEGQQSRPYHAIKSIVKKDMLLK-------LIKAVSTELQAH 217
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
4-172 |
1.19e-67 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 206.18 E-value: 1.19e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRLTgRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:COG0847 3 VVLDTETTGLDP-AKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGQQDRsdvteYCSVLDTLLMARERHPG-QRNNLDALCKRYGVDNSGRdlHGALLDAEI 162
Cdd:COG0847 81 AVLVAHNAAFDLGFLNAELRRAGLPLP-----PFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAEA 153
|
170
....*....|
gi 15597013 163 LADVYLAMTG 172
Cdd:COG0847 154 TAELFLALLR 163
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
4-170 |
1.83e-51 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 165.32 E-value: 1.83e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIR 82
Cdd:COG2176 11 VVFDLETTGLsPKKD--EIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 83 GAQLIIHNAAFDIGFINNEFALLGQQDRsdvteyCSVLDTLLMARERHPGQRN-NLDALCKRYGVDNSGRdlHGALLDAE 161
Cdd:COG2176 88 DAVLVAHNASFDLGFLNAALKRLGLPFD------NPVLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGDAE 159
|
....*....
gi 15597013 162 ILADVYLAM 170
Cdd:COG2176 160 ATAELFLKL 168
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
4-172 |
1.99e-50 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 162.47 E-value: 1.99e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRlTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:smart00479 3 VVIDCETTGLDP-GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHN-AAFDIGFINNEFALLGQQDRSDvteyCSVLDTLLMARERHPG-QRNNLDALCKRYGVDNSGRdLHGALLDAE 161
Cdd:smart00479 81 RILVAGNsAHFDLRFLKLEHPRLGIKQPPK----LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155
|
170
....*....|.
gi 15597013 162 ILADVYLAMTG 172
Cdd:smart00479 156 ATAKLFKKLLE 166
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
4-168 |
1.43e-46 |
|
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: 152.07 E-value: 1.43e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTdGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:cd06127 1 VVFDTETTGLDPK-KDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGQQDRSdvteyCSVLDTLLMARERHPGQRNNL--DALCKRYGVDNSGRdlHGALLDAE 161
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLP-----NPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALADAL 152
|
....*..
gi 15597013 162 ILADVYL 168
Cdd:cd06127 153 ATAELLL 159
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-167 |
1.63e-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: 1.63e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRL-TGRHFHVYLQPDR--EVDEGAIAVHGITNEYLKDKPRFREVANDFFEF 80
Cdd:pfam00929 1 VVIDLETTGLDP-EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 81 IR-GAQLIIHNAAFDIGFINNEFALLGQqdrSDVTEYCSVLDTLLMARERHPGQRNN-LDALCKRYGVDNSGRdLHGALL 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLK---KPMPKLNPVIDTLILDKATYKELPGRsLDALAEKLGLEHIGR-AHRALD 155
|
....*....
gi 15597013 159 DAEILADVY 167
Cdd:pfam00929 156 DARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
4-170 |
2.08e-28 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 113.01 E-value: 2.08e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIR 82
Cdd:PRK00448 422 VVFDVETTGLsAVYD--EIIEIGAVKIKNGEIIDK-FEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCG 498
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 83 GAQLIIHNAAFDIGFINNEFALLGQQDRSdvteyCSVLDTLLMARERHPGQRN-NLDALCKRYGV--DNSgrdlHGALLD 159
Cdd:PRK00448 499 DSILVAHNASFDVGFINTNYEKLGLEKIK-----NPVIDTLELSRFLYPELKShRLNTLAKKFGVelEHH----HRADYD 569
|
170
....*....|.
gi 15597013 160 AEILADVYLAM 170
Cdd:PRK00448 570 AEATAYLLIKF 580
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
4-164 |
1.86e-25 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 100.13 E-value: 1.86e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:PRK07740 62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGA 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINnefALLGQQDRSDVTEycSVLDT-LLMARERHPGQRNNLDALCKRYGVDNSGRdlHGALLDAEI 162
Cdd:PRK07740 142 GVLVAHHAGHDKAFLR---HALWRTYRQPFTH--RLIDTmFLTKLLAHERDFPTLDDALAYYGIPIPRR--HHALGDALM 214
|
..
gi 15597013 163 LA 164
Cdd:PRK07740 215 TA 216
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-170 |
7.58e-24 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 100.03 E-value: 7.58e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 1 MRSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEF 80
Cdd:PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILER-FSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 81 IRGAQLIIHNAAFDIGFINNEFALLGQQDRSdvteyCSVLDTLLMARERHPGQRN-NLDALCKRYGVDNSgrDLHGALLD 159
Cdd:PRK08074 82 LEGAYFVAHNVHFDLNFLNEELERAGYTEIH-----CPKLDTVELARILLPTAESyKLRDLSEELGLEHD--QPHRADSD 154
|
170
....*....|.
gi 15597013 160 AEILADVYLAM 170
Cdd:PRK08074 155 AEVTAELFLQL 165
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
4-178 |
3.43e-20 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 86.04 E-value: 3.43e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDgHRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:PRK06310 10 VCLDCETTGLDVKK-DRIIEFAAIRFTFDEVIDS-VEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLII-HNAAFDIGFINNEFALLGQqdrSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRdlHGALLDAEI 162
Cdd:PRK06310 88 GDYIVgHSVGFDLQVLSQESERIGE---TFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--HRAMKDVEI 162
|
170
....*....|....*.
gi 15597013 163 LADVYLAMTGGQTSLS 178
Cdd:PRK06310 163 NIKVFKHLCKRFRTLE 178
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
4-168 |
6.90e-20 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 86.41 E-value: 6.90e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIR 82
Cdd:PRK06807 11 VVIDFETTGFnPYND--KIIQVAAVKYRNHELVDQ-FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLH 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 83 GAQLIIHNAAFDIGFINNEFALLGQQDRSDVteycsVLDTLLMARERHPGQRNNLDALCKRY-GVDNSGrdlHGALLDAE 161
Cdd:PRK06807 88 TNVIVAHNASFDMRFLKSNVNMLGLPEPKNK-----VIDTVFLAKKYMKHAPNHKLETLKRMlGIRLSS---HNAFDDCI 159
|
....*..
gi 15597013 162 ILADVYL 168
Cdd:PRK06807 160 TCAAVYQ 166
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
4-166 |
2.08e-19 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 85.14 E-value: 2.08e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPvTDGHRIIEIGCVELEGRRLTGRHFHVYLQPdrEVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:PRK06063 18 AVVDVETSGFR-PGQARIISLAVLGLDADGNVEQSVVTLLNP--GVDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGQQDRSDvteycSVLDTLLMARERHPGQRN-NLDALCKRYGVDNsgRDLHGALLDAEI 162
Cdd:PRK06063 95 RTLVAHNVAFDYSFLAAEAERAGAELPVD-----QVMCTVELARRLGLGLPNlRLETLAAHWGVPQ--QRPHDALDDARV 167
|
....
gi 15597013 163 LADV 166
Cdd:PRK06063 168 LAGI 171
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
4-169 |
3.31e-18 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 83.04 E-value: 3.31e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPvTDGHRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:PRK07883 18 VVVDLETTGGS-PAGDAITEIGAVKVRGGEVLGE-FATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARG 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFINNEFALLGqqdrsDVTEYCSVLDTLLMARERHPGQ---RNNLDALCKRYGVDNSGRdlHGALLDA 160
Cdd:PRK07883 96 AVLVAHNAPFDIGFLRAAAARCG-----YPWPGPPVLCTVRLARRVLPRDeapNVRLSTLARLFGATTTPT--HRALDDA 168
|
....*....
gi 15597013 161 EILADVYLA 169
Cdd:PRK07883 169 RATVDVLHG 177
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
4-174 |
6.42e-17 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 76.48 E-value: 6.42e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCVELEGRR-LTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFI 81
Cdd:PRK09145 32 VALDCETTGLdPRRA--EIVSIAAVKIRGNRiLTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 82 RGAQLIIHNAAFDIGFINNE-FALLGQQDRSDVTEYCSVLDTLLMARERHPGQRNNLDALCKRYGVDNSGRdlHGALLDA 160
Cdd:PRK09145 110 GNRPLVGYYLEFDVAMLNRYvRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLGR--HDALNDA 187
|
170
....*....|....
gi 15597013 161 EILADVYLAMTGGQ 174
Cdd:PRK09145 188 IMAALIFLRLRKGD 201
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
7-172 |
3.55e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 74.85 E-value: 3.55e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 7 DTETTGMPVtDGHRIIEIGCVElegrRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG-AQ 85
Cdd:PRK06309 8 DTETTGTQI-DKDRIIEIAAYN----GVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTdNI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 86 LIIHNA-AFDIGFINNEF---ALLGQQDRSdvteycsvLDTLLMARERHPG-QRNNLDALCKRYGVDNSgrDLHGALLDA 160
Cdd:PRK06309 83 LVAHNNdAFDFPLLRKECrrhGLEPPTLRT--------IDSLKWAQKYRPDlPKHNLQYLRQVYGFEEN--QAHRALDDV 152
|
170
....*....|..
gi 15597013 161 EILADVYLAMTG 172
Cdd:PRK06309 153 ITLHRVFSALVG 164
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
4-169 |
9.38e-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: 72.16 E-value: 9.38e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETtgmPVTDGHRIIEIGCVELEGRRLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:cd06130 2 VAIDFET---ANADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGfinnefALLGQQDRSDVTEY-CSVLDTLLMARERHPGQRN-NLDALCKRYGVdnsgrDL--HGALLD 159
Cdd:cd06130 78 SLVVAHNASFDRS------VLRAALEAYGLPPPpYQYLCTVRLARRVWPLLPNhKLNTVAEHLGI-----ELnhHDALED 146
|
170
....*....|
gi 15597013 160 AEILADVYLA 169
Cdd:cd06130 147 ARACAEILLA 156
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
4-163 |
2.53e-14 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 70.44 E-value: 2.53e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGmPVTDGHRIIEIGCVELEGRRLTGRhFHVYLQPDrEVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRG 83
Cdd:PRK08517 71 CFVDIETNG-SKPKKHQIIEIGAVKVKNGEIIDR-FESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGD 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 84 AQLIIHNAAFDIGFIN---NEFALLGQQDRSdvteycsvLDTLLMARERHPGQRNNLDALCKRYGVDN--SGRDLHGALL 158
Cdd:PRK08517 148 SVFVAHNVNFDYNFISrslEEIGLGPLLNRK--------LCTIDLAKRTIESPRYGLSFLKELLGIEIevHHRAYADALA 219
|
....*
gi 15597013 159 DAEIL 163
Cdd:PRK08517 220 AYEIF 224
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
4-170 |
2.37e-10 |
|
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: 57.62 E-value: 2.37e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETT----GMPVTDGHRIIEIGCVELEGR-RLTGRHFHVYLQPDR--EVDEGAIAVHGITNEYLKDKPRFREVAND 76
Cdd:cd06133 2 LVIDFEATcwegNSKPDYPNEIIEIGAVLVDVKtKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 77 FFEFIRGAQliihNAAF------DIGFINNEFALLGQQDRSDV-TEYCSVLDtlLMARERHPGQRNNLDALCKRYGVDNS 149
Cdd:cd06133 82 FLEWLGKNG----KYAFvtwgdwDLKDLLQNQCKYKIINLPPFfRQWIDLKK--EFAKFYGLKKRTGLSKALEYLGLEFE 155
|
170 180
....*....|....*....|.
gi 15597013 150 GRdLHGALLDAEILADVYLAM 170
Cdd:cd06133 156 GR-HHRGLDDARNIARILKRL 175
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
4-160 |
3.22e-10 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 58.45 E-value: 3.22e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDGhRIIE--IGCVELEGRRLTGRHFhvYLQPDREVDEGAIAVHGITNEYLKDKPR-----FREVAND 76
Cdd:PRK07942 9 AAFDLETTGVDPETA-RIVTaaLVVVDADGEVVESREW--LADPGVEIPEEASAVHGITTEYARAHGRpaaevLAEIADA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 77 FFE-FIRGAQLIIHNAAFDigfinneFALLGQQDRSDVTEYCS---VLDTLLMARERHP---GQRnNLDALCKRYGV--D 147
Cdd:PRK07942 86 LREaWARGVPVVVFNAPYD-------LTVLDRELRRHGLPSLVpgpVIDPYVIDKAVDRyrkGKR-TLTALCEHYGVrlD 157
|
170
....*....|...
gi 15597013 148 NSgrdlHGALLDA 160
Cdd:PRK07942 158 NA----HEATADA 166
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
2-177 |
2.40e-09 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 57.00 E-value: 2.40e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 2 RSVVLDTETTGMPVTdgHRIIEIGCVELEGRRLTgRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFI 81
Cdd:PRK07246 8 KYAVVDLEATGAGPN--ASIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 82 RGAQLIIHNAAFDIGFINNEFALLGQQDRSdvteycSVLDTLLMARERHPG-QRNNLDALCKRYGVDNSgrDLHGALLDA 160
Cdd:PRK07246 85 EDCIFVAHNVKFDANLLAEALFLEGYELRT------PRVDTVELAQVFFPTlEKYSLSHLSRELNIDLA--DAHTAIADA 156
|
170
....*....|....*..
gi 15597013 161 EILADVYLAMTGGQTSL 177
Cdd:PRK07246 157 RATAELFLKLLQKIESL 173
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
4-134 |
1.82e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 53.39 E-value: 1.82e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVtDGHRIIEIGCVELEGRRLTGRH-FHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIR 82
Cdd:PRK09146 50 VALDFETTGLDA-EQDAIVSIGLVPFTLQRIRCRQaRHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALA 128
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 15597013 83 GAQLIIHNAAFDIGFINNefALlgqqdRSDVTEYC--SVLDTLLMARERHPGQR 134
Cdd:PRK09146 129 GKVVVVHYRRIERDFLDQ--AL-----RNRIGEGIefPVIDTMEIEARIQRKQA 175
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
4-171 |
4.88e-08 |
|
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: 51.52 E-value: 4.88e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDGhrIIEIGCVEL----EGRRLTGR--HFHVYLQPDREVDEGAIAVHGITneylKDKP-RF----R 71
Cdd:cd06134 8 VVVDVETGGFnPQTDA--LLEIAAVTLemdeQGNLYPDEtfHFHILPFEGANLDPAALEFNGID----PFHPfRFavdeK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 72 EVANDFFEFIRGAQ---------LIIHNAAFDIGFINNEFALLGQQdRSDVTEYcSVLDTLLMARERHpGQrNNLDALCK 142
Cdd:cd06134 82 EALKEIFKPIRKALkaqgctraiLVGHNAHFDLGFLNAAVARCKIK-RNPFHPF-STFDTATLAGLAY-GQ-TVLAKACQ 157
|
170 180
....*....|....*....|....*....
gi 15597013 143 RYGVDNSGRDLHGALLDAEILADVYLAMT 171
Cdd:cd06134 158 AAGIEFDNKEAHSALYDTQKTAELFCKIV 186
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
4-98 |
5.57e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 52.29 E-value: 5.57e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCV----ELEGR--RLTGRhFHVYLQPDREVDEGAIAVHGITNEYLKDK--PRfREVA 74
Cdd:PRK09182 40 VILDTETTGLdPRKD--EIIEIGMVafeyDDDGRigDVLDT-FGGLQQPSRPIPPEITRLTGITDEMVAGQtiDP-AAVD 115
|
90 100
....*....|....*....|....*
gi 15597013 75 ndffEFIRGAQLII-HNAAFDIGFI 98
Cdd:PRK09182 116 ----ALIAPADLIIaHNAGFDRPFL 136
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
5-94 |
1.65e-06 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 47.41 E-value: 1.65e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 5 VLDTETTGMpvtDGHrIIEIGCVELEGRRLTGRHFHVyLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFefirGA 84
Cdd:PRK07983 4 VIDTETCGL---QGG-IVEIASVDVIDGKIVNPMSHL-VRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY----GS 74
|
90
....*....|.
gi 15597013 85 QL-IIHNAAFD 94
Cdd:PRK07983 75 EWyVAHNASFD 85
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
4-102 |
1.82e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 48.29 E-value: 1.82e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGM-PVTDghRIIEIGCVELEGRRLTGRHFHVYLQPdrEVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIR 82
Cdd:PRK05601 49 VAVSIQTSGIhPSTS--RLITIDAVTLTADGEEVEHFHAVLNP--GEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLID 124
|
90 100
....*....|....*....|
gi 15597013 83 GAQLIIHNAAFDIGFINNEF 102
Cdd:PRK05601 125 GRTLILHNAPRTWGFIVSEA 144
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
4-144 |
1.64e-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: 41.17 E-value: 1.64e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMPVTDGHRIIEIGCVELEGRRL--TGRH----------FHVYLQPDREVDEGAIAVHGITNEYLKDKPRF- 70
Cdd:cd06136 2 VFLDLETTGLPKHNRPEITELCLVAVHRDHLlnTSRDkpalprvldkLSLCFNPGRAISPGASEITGLSNDLLEHKAPFd 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15597013 71 REVANDFFEFIRGAQ----LIIHNA-AFDIGFINNEFALLGQQDRSDVteYCsvLDTLLMARERHpgqrNNLDALCKRY 144
Cdd:cd06136 82 SDTANLIKLFLRRQPkpicLVAHNGnRFDFPILRSELERLGTKLPDDI--LC--VDSLPAFRELD----QSLGSLYKRL 152
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
54-100 |
3.10e-04 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 41.30 E-value: 3.10e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 15597013 54 IAVHGITNEYLKDKPRFREVANDFFEFIRGAQLIIHNAAFDIGFINN 100
Cdd:PRK06195 51 IGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRK 97
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
2-78 |
3.32e-04 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 41.24 E-value: 3.32e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15597013 2 RSVVLDTETTGMPVTDgHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEgAIAVHGITNEYLKDKPRFREVANDFF 78
Cdd:pfam13361 187 NIVVFDVETTGLDTTE-DEIIQIAAIKLNKKGVVIESFERFLRLKKPVGD-SLQVHGFSDEFLQENGETPAEALRDF 261
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
2-106 |
2.99e-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: 37.62 E-value: 2.99e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 2 RSVVLDTETTGMpVTDGHRIIEIGCVELEGRRLTGRhfhVYLQPDREvDEGAIavhgitneyLKdkprfrevanDFFEFI 81
Cdd:COG3359 16 DLLFFDIETTGL-SGGGTVIFLIGLADGEGDGFVVR---QYFGEDPG-EEAAL---------LE----------AFLEWL 71
|
90 100
....*....|....*....|....*..
gi 15597013 82 RGAQLIIH-N-AAFDIGFINNEFALLG 106
Cdd:COG3359 72 ADYKLLVTyNgKSFDLPFLKTRFTLHR 98
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
39-89 |
3.62e-03 |
|
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: 36.72 E-value: 3.62e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 15597013 39 FHVYLQPDREVDEGAIAVHGITNEYLKDKPRFREVANDFFEFIRGAQLIIH 89
Cdd:cd06144 33 YDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGH 83
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
4-109 |
8.25e-03 |
|
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: 36.25 E-value: 8.25e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15597013 4 VVLDTETTGMpvtdGHR--IIEIGCVELEGRR-LTGRHFHVYLQPDREVDEGAIAVHGITNEYLK------------DKP 68
Cdd:pfam16473 3 LMIDIETLGN----EPTapIVSIGAVFFDPETgELGKEFYARIDLESSMSAGATIDADTILWWLKqssearaqllgdDAP 78
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 15597013 69 RFREVANDFFEFIR------GAQLIIHNAAFDIGFINNEFALLGQQD 109
Cdd:pfam16473 79 SLPDALLDLNDFIRdngdpkSLKVWGNGASFDNVILRAAFERGGLPA 125
|
|
| |
