|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-245 |
1.82e-177 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 486.67 E-value: 1.82e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 6 TGITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 86 ADEFLDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 166 GALLDAQILADVYLMMTGGQTTMAFSIEGDSQQQNDTG-IQRIVRQSSKLRVVFATDEELAAHESRLDLVQKKGGSCLWR 244
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEEtIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1069082775 245 A 245
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
10-238 |
3.79e-117 |
|
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: 333.98 E-value: 3.79e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1069082775 170 DAQILADVYLMMTGGQTTMAFSIEGDSQQQNDTGIQRIVRQSSKLRVVFATDEELAAHESRLDLVQKKG 238
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQESLLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
11-182 |
1.11e-109 |
|
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: 312.54 E-value: 1.11e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFL 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 91 DYIRGAELVIHNASFDIGFMDYEFAKLkRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1069082775 171 AQILADVYLMMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
5.61e-68 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 206.95 E-value: 5.61e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKtnefCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1069082775 169 LDAQILADVYLMMTG 183
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
10-183 |
1.54e-48 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 157.46 E-value: 1.54e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHN-ASFDIGFMDYEFAKLKRDIPKTNEfckITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP---VIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1069082775 168 LLDAQILADVYLMMTG 183
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
12-178 |
3.74e-44 |
|
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: 146.34 E-value: 3.74e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 89 FLDYIR-GAELVIHNASFDIGFMDYEFAK-LKRDIPKTNEFCkitDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtLH 165
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKRfLKKPMPKLNPVI---DTLILDKATYKElPGRSLDALAEKLGLEHIGR-AH 151
|
170
....*....|...
gi 1069082775 166 GALLDAQILADVY 178
Cdd:pfam00929 152 RALDDARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-245 |
1.82e-177 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 486.67 E-value: 1.82e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 6 TGITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 86 ADEFLDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 166 GALLDAQILADVYLMMTGGQTTMAFSIEGDSQQQNDTG-IQRIVRQSSKLRVVFATDEELAAHESRLDLVQKKGGSCLWR 244
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEEtIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1069082775 245 A 245
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
10-238 |
3.79e-117 |
|
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: 333.98 E-value: 3.79e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1069082775 170 DAQILADVYLMMTGGQTTMAFSIEGDSQQQNDTGIQRIVRQSSKLRVVFATDEELAAHESRLDLVQKKG 238
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQESLLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
11-182 |
1.11e-109 |
|
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: 312.54 E-value: 1.11e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFL 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 91 DYIRGAELVIHNASFDIGFMDYEFAKLkRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1069082775 171 AQILADVYLMMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
9-227 |
3.50e-106 |
|
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: 305.91 E-value: 3.50e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:TIGR00573 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 89 FLDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGAL 168
Cdd:TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 1069082775 169 LDAQILADVYLMMTGGQTTMaFSIEGDSQQQNDTgIQRIVRQSSKLRVVFATDEELAAH 227
Cdd:TIGR00573 161 ADAFILAKLYLVMTGKQTKY-GENEGQQSRPYHA-IKSIVKKDMLLKLIKAVSTELQAH 217
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
5.61e-68 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 206.95 E-value: 5.61e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKtnefCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1069082775 169 LDAQILADVYLMMTG 183
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
10-183 |
1.54e-48 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 157.46 E-value: 1.54e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHN-ASFDIGFMDYEFAKLKRDIPKTNEfckITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP---VIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1069082775 168 LLDAQILADVYLMMTG 183
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
12-181 |
3.38e-47 |
|
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: 3.38e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLD 91
Cdd:COG2176 11 VVFDLETTGLS-----PKKDEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 92 YIRGAELVIHNASFDIGFMDYEFAKLKRDIPktNEFCkitDSLALARKMFPGKRN-SLDALCSRYEIDNSKRtlHGALLD 170
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFD--NPVL---DTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGD 157
|
170
....*....|.
gi 1069082775 171 AQILADVYLMM 181
Cdd:COG2176 158 AEATAELFLKL 168
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
12-179 |
1.19e-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: 152.45 E-value: 1.19e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLD 91
Cdd:cd06127 1 VVFDTETTGLD-----PKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 92 YIRGAELVIHNASFDIGFMDYEFAKLKRDIPKtnefCKITDSLALARKMFPGKRNSL--DALCSRYEIDNSKRtlHGALL 169
Cdd:cd06127 76 FLGGRVLVAHNASFDLRFLNRELRRLGGPPLP----NPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALA 149
|
170
....*....|
gi 1069082775 170 DAQILADVYL 179
Cdd:cd06127 150 DALATAELLL 159
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
12-178 |
3.74e-44 |
|
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: 146.34 E-value: 3.74e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 89 FLDYIR-GAELVIHNASFDIGFMDYEFAK-LKRDIPKTNEFCkitDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtLH 165
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKRfLKKPMPKLNPVI---DTLILDKATYKElPGRSLDALAEKLGLEHIGR-AH 151
|
170
....*....|...
gi 1069082775 166 GALLDAQILADVY 178
Cdd:pfam00929 152 RALDDARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
13-181 |
5.76e-26 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 106.08 E-value: 5.76e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 13 VLDTETTGMNqigAHYegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLDY 92
Cdd:PRK00448 423 VFDVETTGLS---AVY--DEIIEIGAVKIKNGEII-DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEF 496
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 93 IRGAELVIHNASFDIGFMDYEFAKLKRDIPKtnefCKITDSLALARKMFPG-KRNSLDALCSRYEI--DNSkrtlHGALL 169
Cdd:PRK00448 497 CGDSILVAHNASFDVGFINTNYEKLGLEKIK----NPVIDTLELSRFLYPElKSHRLNTLAKKFGVelEHH----HRADY 568
|
170
....*....|..
gi 1069082775 170 DAQILADVYLMM 181
Cdd:PRK00448 569 DAEATAYLLIKF 580
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
13-177 |
1.64e-19 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 86.90 E-value: 1.64e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 13 VLDTETTGmnqigAHYEGHKIIEIGAV-----EVVNRRLTgnnfhvylkpdrLVDPE----AFGVH--GIADEFLLDKPT 81
Cdd:PRK07883 19 VVDLETTG-----GSPAGDAITEIGAVkvrggEVLGEFAT------------LVNPGrpipPFITVltGITTAMVAGAPP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 82 FADVADEFLDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTnefcKITDSLALARKMFP--GKRN-SLDALCSRYEID 158
Cdd:PRK07883 82 IEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGP----PVLCTVRLARRVLPrdEAPNvRLSTLARLFGAT 157
|
170
....*....|....*....
gi 1069082775 159 NSKRtlHGALLDAQILADV 177
Cdd:PRK07883 158 TTPT--HRALDDARATVDV 174
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
10-181 |
9.19e-19 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 85.00 E-value: 9.19e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGmNQIGahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:PRK08074 4 RFVVVDLETTG-NSPK---KGDKIIQIAAVVVEDGEIL-ERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 90 LDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKtnefCKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKRtlHGAL 168
Cdd:PRK08074 79 VELLEGAYFVAHNVHFDLNFLNEELERAGYTEIH----CPKLDTVELARILLPTAESyKLRDLSEELGLEHDQP--HRAD 152
|
170
....*....|...
gi 1069082775 169 LDAQILADVYLMM 181
Cdd:PRK08074 153 SDAEVTAELFLQL 165
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
12-179 |
1.70e-18 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 82.55 E-value: 1.70e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQIGahyegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLD 91
Cdd:PRK06807 11 VVIDFETTGFNPYN-----DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 92 YIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTnefcKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKrtlHGALLD 170
Cdd:PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN----KVIDTVFLAKKYMKHAPNhKLETLKRMLGIRLSS---HNAFDD 157
|
....*....
gi 1069082775 171 AQILADVYL 179
Cdd:PRK06807 158 CITCAAVYQ 166
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
12-175 |
2.78e-18 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 80.87 E-value: 2.78e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLD 91
Cdd:PRK07740 62 VVFDLETTGFS----PQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 92 YIRGAELVIHNASFDIGFMDYEFAKLKRdIPKTNefcKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKRtlHGALLD 170
Cdd:PRK07740 138 FIGAGVLVAHHAGHDKAFLRHALWRTYR-QPFTH---RLIDTMFLTKLLAHERDFpTLDDALAYYGIPIPRR--HHALGD 211
|
....*
gi 1069082775 171 AQILA 175
Cdd:PRK07740 212 ALMTA 216
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
12-179 |
5.35e-18 |
|
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: 77.94 E-value: 5.35e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETtgmnqigAHYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLD 91
Cdd:cd06130 2 VAIDFET-------ANADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 92 YIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCkitdSLALARKMFPGKRN-SLDALCSRYEIDnskrtL--HGAL 168
Cdd:cd06130 74 FLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLC----TVRLARRVWPLLPNhKLNTVAEHLGIE-----LnhHDAL 144
|
170
....*....|.
gi 1069082775 169 LDAQILADVYL 179
Cdd:cd06130 145 EDARACAEILL 155
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
13-177 |
3.06e-17 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 78.97 E-value: 3.06e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 13 VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDrlVDPEAFGVHGIADEFLLDKPTFADVADEFLDY 92
Cdd:PRK06063 19 VVDVETSGFRP-----GQARIISLAVLGLDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 93 IRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCkitdSLALARKMFPGKRN-SLDALCSRYEIdnSKRTLHGALLDA 171
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMC----TVELARRLGLGLPNlRLETLAAHWGV--PQQRPHDALDDA 165
|
....*.
gi 1069082775 172 QILADV 177
Cdd:PRK06063 166 RVLAGI 171
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
8-183 |
2.52e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 75.23 E-value: 2.52e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 8 ITRQIVLDTETTGMnQIgahyEGHKIIEIGAVEVVnrrlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVAD 87
Cdd:PRK06309 1 MPALIFYDTETTGT-QI----DKDRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQ 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 88 EFLDYIRG-AELVIHNA-SFDIGFMDYEFAKLKRDIPKTnefcKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtl 164
Cdd:PRK06309 72 KFIEFCGTdNILVAHNNdAFDFPLLRKECRRHGLEPPTL----RTIDSLKWAQKYRPDlPKHNLQYLRQVYGFEENQA-- 145
|
170
....*....|....*....
gi 1069082775 165 HGALLDAQILADVYLMMTG 183
Cdd:PRK06309 146 HRALDDVITLHRVFSALVG 164
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
12-185 |
1.00e-14 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 70.32 E-value: 1.00e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQIGAHyeghkIIEIGAVEVV-NRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFL 90
Cdd:PRK09145 32 VALDCETTGLDPRRAE-----IVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 91 DYIRGAELVIHNASFDIGFMD-YEFAKLKRDIPktNEfcKITDSLALARKMFPGKRN-----SLDALCSRYEIDNSKRtl 164
Cdd:PRK09145 107 AFIGNRPLVGYYLEFDVAMLNrYVRPLLGIPLP--NP--LIEVSALYYDKKERHLPDayidlRFDAILKHLDLPVLGR-- 180
|
170 180
....*....|....*....|.
gi 1069082775 165 HGALLDAQILADVYLMMTGGQ 185
Cdd:PRK09145 181 HDALNDAIMAALIFLRLRKGD 201
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
13-186 |
7.83e-14 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 68.21 E-value: 7.83e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 13 VLDTETTGMnqigahyEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLdy 92
Cdd:PRK07983 4 VIDTETCGL-------QG-GIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY-- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 93 irGAEL-VIHNASFDigfmdyefaklKRDIPKTNE--FCkitdSLALARKMFPGKRNSLDALcsRYEIDNSKRT-----L 164
Cdd:PRK07983 73 --GSEWyVAHNASFD-----------RRVLPEMPGewIC----TMKLARRLWPGIKYSNMAL--YKSRKLNVQTppglhH 133
|
170 180
....*....|....*....|....
gi 1069082775 165 HGALLDAQILAD--VYLMMTGGQT 186
Cdd:PRK07983 134 HRALYDCYITAAllIDIMNTSGWT 157
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
12-188 |
3.28e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 61.38 E-value: 3.28e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQigahyEGHKIIEIGAVevvnrRLTGNN----FHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVAD 87
Cdd:PRK06310 10 VCLDCETTGLDV-----KKDRIIEFAAI-----RFTFDEvidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 88 EFLDYIRGAELVI-HNASFDIGFMDYEFAKLkrDIPKTNEFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRtlHG 166
Cdd:PRK06310 80 QIKGFFKEGDYIVgHSVGFDLQVLSQESERI--GETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--HR 155
|
170 180
....*....|....*....|..
gi 1069082775 167 ALLDAQILADVYLMMTGGQTTM 188
Cdd:PRK06310 156 AMKDVEINIKVFKHLCKRFRTL 177
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
6-171 |
2.00e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 59.27 E-value: 2.00e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 6 TGITRQI--VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLvdPEAFG-VHGIADEFLLDKPTF 82
Cdd:PRK08517 63 TPIKDQVfcFVDIETNGSKP-----KKHQIIEIGAVKVKNGEII-DRFESFVKAKEV--PEYITeLTGITYEDLENAPSL 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 83 ADVADEFLDYIRGAELVIHNASFDIGFMDYEFAKLKRDIPKTNEFCKITdslaLARKMFPGKRNSLDALCSRYEIDNSkr 162
Cdd:PRK08517 135 KEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTID----LAKRTIESPRYGLSFLKELLGIEIE-- 208
|
....*....
gi 1069082775 163 TLHGALLDA 171
Cdd:PRK08517 209 VHHRAYADA 217
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
10-110 |
2.91e-07 |
|
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: 50.48 E-value: 2.91e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTETTGMNQIGAhyeghKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVdPEAFGVHGIADEFLLDKP-TFADVADE 88
Cdd:pfam13361 187 NIVVFDVETTGLDTTED-----EIIQIAAIKLNKKGVVIESFERFLRLKKPV-GDSLQVHGFSDEFLQENGeTPAEALRD 260
|
90 100
....*....|....*....|...
gi 1069082775 89 FLDYIRG-AELVIHNASFDIGFM 110
Cdd:pfam13361 261 FLEKLENlRELYSILREYDDIEE 283
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
12-111 |
3.30e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 49.97 E-value: 3.30e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQigahyEGHKIIEIGAV-----------EVVNRrltgnnFHVYLKPDRLVDPEAFGVHGIADEFLLDKP 80
Cdd:PRK09182 40 VILDTETTGLDP-----RKDEIIEIGMVafeydddgrigDVLDT------FGGLQQPSRPIPPEITRLTGITDEMVAGQT 108
|
90 100 110
....*....|....*....|....*....|..
gi 1069082775 81 TFADVADEFLDyirGAELVI-HNASFDIGFMD 111
Cdd:PRK09182 109 IDPAAVDALIA---PADLIIaHNAGFDRPFLE 137
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
12-177 |
3.78e-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: 48.76 E-value: 3.78e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQIGAHYEGHKIIEIGAVEV-VNRRLTGNNFHVYLKPdrLVDPEAF----GVHGIADEFLLDKPTFADVA 86
Cdd:cd06133 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVdVKTKEIIDTFSSYVKP--VINPKLSdfctELTGITQEDVDNAPSFPEVL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 87 DEFLDYIR---GAELVIhNASFDIGFMDYEFAKLKRD--IPKTNEFCKITDSLALARKMfpGKRNSLDALCSRYEIDNSK 161
Cdd:cd06133 80 KEFLEWLGkngKYAFVT-WGDWDLKDLLQNQCKYKIInlPPFFRQWIDLKKEFAKFYGL--KKRTGLSKALEYLGLEFEG 156
|
170
....*....|....*.
gi 1069082775 162 RTlHGALLDAQILADV 177
Cdd:cd06133 157 RH-HRGLDDARNIARI 171
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
14-111 |
1.06e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 48.38 E-value: 1.06e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 14 LDTETTGMNQigahyEGHKIIEIGAVEV-VNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFLDY 92
Cdd:PRK09146 52 LDFETTGLDA-----EQDAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126
|
90
....*....|....*....
gi 1069082775 93 IRGAELVIHNASFDIGFMD 111
Cdd:PRK09146 127 LAGKVVVVHYRRIERDFLD 145
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
12-181 |
1.16e-06 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 48.05 E-value: 1.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQIGAHYEGHKIIEIGAV-EVVNRRltgnnfhvylkpDRLVDP------EAFGVHGIADEFL-LDKPTFA 83
Cdd:PRK07942 9 AAFDLETTGVDPETARIVTAALVVVDADgEVVESR------------EWLADPgveipeEASAVHGITTEYArAHGRPAA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 84 DVADEFLDYIR-----GAELVIHNASFDIGFMDYEfakLKRDIPKTNEFCKITDSLALARKMFP---GKRNsLDALCSRY 155
Cdd:PRK07942 77 EVLAEIADALReawarGVPVVVFNAPYDLTVLDRE---LRRHGLPSLVPGPVIDPYVIDKAVDRyrkGKRT-LTALCEHY 152
|
170 180
....*....|....*....|....*...
gi 1069082775 156 EI--DNSkrtlHGALLDAQILADVYLMM 181
Cdd:PRK07942 153 GVrlDNA----HEATADALAAARVAWAL 176
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
36-146 |
3.75e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 47.08 E-value: 3.75e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 36 IGAVEVVNRRLTGNNFHVyLKPDRLV-DPEAFGVHGIADEFLLDKPTFADVADEFLDYIRGAELVIHNASFDIGFMDYEF 114
Cdd:PRK06195 21 IGIVVVKDGEIVEKVHYL-IKPKEMRfMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTL 99
|
90 100 110
....*....|....*....|....*....|..
gi 1069082775 115 AKLKRDIPKTNEFCkitdSLALARKMFPGKRN 146
Cdd:PRK06195 100 ELYNIPMPSFEYIC----TMKLAKNFYSNIDN 127
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
10-183 |
2.10e-05 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 43.69 E-value: 2.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 10 RQIVLDTEttgMNQI-GAHYEGHK--IIEIGAVEV-VNRRLTGnNFHVYLKPDR--LVDPEAFGVHGIADEFLLDKPTFA 83
Cdd:COG5018 3 KYLVIDLE---ATCWdGKPPPGFPmeIIEIGAVKVdENGEIID-EFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 84 DVADEFLDYIRGAELVIhnASFdiGFMD--------------YEFAKLKRDIPKtnEFCKITDSlalarkmfpGKRNSLD 149
Cdd:COG5018 79 EAIEDFKKWIGSEDYIL--CSW--GDYDrkqlerncrfhgvpYPFGDRHINLKK--LFALYFGL---------KKRIGLK 143
|
170 180 190
....*....|....*....|....*....|....
gi 1069082775 150 ALCSRYEIDNsKRTLHGALLDAQILADVYLMMTG 183
Cdd:COG5018 144 KALELLGLEF-EGTHHRALDDARNTAKLFKKILG 176
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
25-125 |
4.14e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 44.05 E-value: 4.14e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 25 GAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFADVADEFLDYIRGAELVIHNAS 104
Cdd:PRK05601 57 GIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGE--DPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAP 134
|
90 100
....*....|....*....|.
gi 1069082775 105 FDIGFMDYEFAKLKRDIPKTN 125
Cdd:PRK05601 135 RTWGFIVSEAKRAMNAAARAN 155
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
12-182 |
4.45e-04 |
|
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: 39.97 E-value: 4.45e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVV----NRRLTGNNFHVYLKP--DRLVDPEAFGVHGI----ADEFLLDKpt 81
Cdd:cd06134 8 VVVDVETGGFNP-----QTDALLEIAAVTLEmdeqGNLYPDETFHFHILPfeGANLDPAALEFNGIdpfhPFRFAVDE-- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 82 fADVADEFLDYIRG---------AELVIHNASFDIGFMDyefAKLKRDIPKTNEFCKIT--DSLALARKMFpGKrNSLDA 150
Cdd:cd06134 81 -KEALKEIFKPIRKalkaqgctrAILVGHNAHFDLGFLN---AAVARCKIKRNPFHPFStfDTATLAGLAY-GQ-TVLAK 154
|
170 180 190
....*....|....*....|....*....|..
gi 1069082775 151 LCSRYEIDNSKRTLHGALLDAQILADVYLMMT 182
Cdd:cd06134 155 ACQAAGIEFDNKEAHSALYDTQKTAELFCKIV 186
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
12-195 |
1.16e-03 |
|
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: 38.47 E-value: 1.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 12 IVLDTETTGMnqigAHYEGHKIIEIGAVeVVNRRLTGNNFHVYLKPDRLVD-------------PEAFGVHGIADEFLLD 78
Cdd:cd06136 2 VFLDLETTGL----PKHNRPEITELCLV-AVHRDHLLNTSRDKPALPRVLDklslcfnpgraisPGASEITGLSNDLLEH 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 79 KPTF----ADVADEFLDYIRGAE-LVIHNAsfdigfMDYEFAKLKRDIPKTNEfckitdslalarkMFPGKRNSLDALCS 153
Cdd:cd06136 77 KAPFdsdtANLIKLFLRRQPKPIcLVAHNG------NRFDFPILRSELERLGT-------------KLPDDILCVDSLPA 137
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1069082775 154 RYEIDnskrtlhgalldaQILADVYLMMTGGQTTMAFSIEGD 195
Cdd:cd06136 138 FRELD-------------QSLGSLYKRLFGQEPKNSHTAEGD 166
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
4-179 |
1.32e-03 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 39.67 E-value: 1.32e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 4 MSTGITRQ-IVLDTETTGmnqigAHYEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTF 82
Cdd:PRK07246 1 MTQKKLRKyAVVDLEATG-----AGPNA-SIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDF 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1069082775 83 ADVADEFLDYIRGAELVIHNASFDIG------FMD-YEFAklkrdIPKtnefckiTDSLALARKMFPG-KRNSLDALCSR 154
Cdd:PRK07246 74 SQVARHIYDLIEDCIFVAHNVKFDANllaealFLEgYELR-----TPR-------VDTVELAQVFFPTlEKYSLSHLSRE 141
|
170 180
....*....|....*....|....*
gi 1069082775 155 YEIDNSKRtlHGALLDAQILADVYL 179
Cdd:PRK07246 142 LNIDLADA--HTAIADARATAELFL 164
|
|
| |
