|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-246 |
1.60e-180 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 494.76 E-value: 1.60e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 6 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 86 ADEFMDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 166 GALLDAQILADVYLMMTGGQTSMAFSMEGESQQQAGEMGIQRVVRAASQLRVVYASDEELVNHESRLDLVQKKGGSCLWR 245
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1031389505 246 A 246
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
10-239 |
3.68e-113 |
|
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: 323.58 E-value: 3.68e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 170 DAQILADVYLMMTGGQTSmAFSMEGESQQQAGEMGIQRVVRAASQLRVVYASDEELVNHESRLDLVQKKG 239
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQES-LLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 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 |
2.14e-110 |
|
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: 314.47 E-value: 2.14e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFM 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 91 DYIRGAELVIHNASFDIGFMDYEFgKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAEL-SLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1031389505 171 AQILADVYLMMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
8.33e-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: 203.87 E-value: 8.33e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVINRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHNASFDIGFMDYEFgklnRGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAEL----RRAGLPLPPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1031389505 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 |
9.24e-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: 155.54 E-value: 9.24e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVINRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHN-ASFDIGFMDYEFgklNRGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1031389505 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 |
2.23e-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: 139.02 E-value: 2.23e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVINRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 89 FMDYIR-GAELVIHNASFDIGFMDYEFGKLnrGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtLHG 166
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKRF--LKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 1031389505 167 ALLDAQILADVY 178
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-246 |
1.60e-180 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 494.76 E-value: 1.60e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 6 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 86 ADEFMDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 166 GALLDAQILADVYLMMTGGQTSMAFSMEGESQQQAGEMGIQRVVRAASQLRVVYASDEELVNHESRLDLVQKKGGSCLWR 245
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1031389505 246 A 246
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
10-239 |
3.68e-113 |
|
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: 323.58 E-value: 3.68e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 170 DAQILADVYLMMTGGQTSmAFSMEGESQQQAGEMGIQRVVRAASQLRVVYASDEELVNHESRLDLVQKKG 239
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQES-LLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 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 |
2.14e-110 |
|
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: 314.47 E-value: 2.14e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFM 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 91 DYIRGAELVIHNASFDIGFMDYEFgKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAEL-SLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1031389505 171 AQILADVYLMMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
9-228 |
2.23e-104 |
|
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: 301.29 E-value: 2.23e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:TIGR00573 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 89 FMDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRTLHGAL 168
Cdd:TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 169 LDAQILADVYLMMTGGQTSMAfsmEGESQQQAGEMGIQRVVRAASQLRVVYASDEELVNH 228
Cdd:TIGR00573 161 ADAFILAKLYLVMTGKQTKYG---ENEGQQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
8.33e-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: 203.87 E-value: 8.33e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVINRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHNASFDIGFMDYEFgklnRGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAEL----RRAGLPLPPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1031389505 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 |
9.24e-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: 155.54 E-value: 9.24e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVINRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 90 MDYIRGAELVIHN-ASFDIGFMDYEFgklNRGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1031389505 168 LLDAQILADVYLMMTG 183
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
12-179 |
2.23e-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: 151.68 E-value: 2.23e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMD 91
Cdd:cd06127 1 VVFDTETTGLD-----PKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 YIRGAELVIHNASFDIGFMDYEFGKLnrgiGKTETFCKITDSLALARKMFPGKRNSL--DALCSRYEIDNSKRtlHGALL 169
Cdd:cd06127 76 FLGGRVLVAHNASFDLRFLNRELRRL----GGPPLPNPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALA 149
|
170
....*....|
gi 1031389505 170 DAQILADVYL 179
Cdd:cd06127 150 DALATAELLL 159
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
12-181 |
4.64e-46 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 151.45 E-value: 4.64e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVINRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMD 91
Cdd:COG2176 11 VVFDLETTGLS-----PKKDEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 YIRGAELVIHNASFDIGFMDYEFGKLNRgigktETFCKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKRtlHGALLD 170
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGL-----PFDNPVLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGD 157
|
170
....*....|.
gi 1031389505 171 AQILADVYLMM 181
Cdd:COG2176 158 AEATAELFLKL 168
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
12-178 |
2.23e-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: 139.02 E-value: 2.23e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVINRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFADVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 89 FMDYIR-GAELVIHNASFDIGFMDYEFGKLnrGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtLHG 166
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKRF--LKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 1031389505 167 ALLDAQILADVY 178
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
13-181 |
2.60e-26 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 107.23 E-value: 2.60e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 13 VLDTETTGMNqigAHYegHKIIEIGAV-----EVINRrltgnnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVAD 87
Cdd:PRK00448 423 VFDVETTGLS---AVY--DEIIEIGAVkikngEIIDK------FEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLP 491
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 88 EFMDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKtetfCKITDSLALARKMFPG-KRNSLDALCSRYEI--DNSkrtl 164
Cdd:PRK00448 492 KFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIK----NPVIDTLELSRFLYPElKSHRLNTLAKKFGVelEHH---- 563
|
170
....*....|....*..
gi 1031389505 165 HGALLDAQILADVYLMM 181
Cdd:PRK00448 564 HRADYDAEATAYLLIKF 580
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
10-181 |
8.00e-20 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 88.09 E-value: 8.00e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGmNQIGahyEGHKIIEIGAV-----EVINRrltgnnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAD 84
Cdd:PRK08074 4 RFVVVDLETTG-NSPK---KGDKIIQIAAVvvedgEILER------FSSFVNPERPIPPFITELTGISEEMVKQAPLFED 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 85 VADEFMDYIRGAELVIHNASFDIGFMDYEFgklnRGIGKTETFCKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKRt 163
Cdd:PRK08074 74 VAPEIVELLEGAYFVAHNVHFDLNFLNEEL----ERAGYTEIHCPKLDTVELARILLPTAESyKLRDLSEELGLEHDQP- 148
|
170
....*....|....*...
gi 1031389505 164 lHGALLDAQILADVYLMM 181
Cdd:PRK08074 149 -HRADSDAEVTAELFLQL 165
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
12-175 |
1.11e-18 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 82.02 E-value: 1.11e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNqigaHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMD 91
Cdd:PRK07740 62 VVFDLETTGFS----PQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 YIRGAELVIHNASFDIGFMDYEFGKLNRgigktETFC-KITDSLALARKMFPGKRN-SLDALCSRYEIDNSKRtlHGALL 169
Cdd:PRK07740 138 FIGAGVLVAHHAGHDKAFLRHALWRTYR-----QPFThRLIDTMFLTKLLAHERDFpTLDDALAYYGIPIPRR--HHALG 210
|
....*.
gi 1031389505 170 DAQILA 175
Cdd:PRK07740 211 DALMTA 216
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
12-179 |
6.61e-18 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 81.01 E-value: 6.61e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQIGahyegHKIIEIGAVEVINRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMD 91
Cdd:PRK06807 11 VVIDFETTGFNPYN-----DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 YIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTetfcKITDSLALARKMFPGKRN-SLDALCSRYEIDNSKrtlHGALLD 170
Cdd:PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN----KVIDTVFLAKKYMKHAPNhKLETLKRMLGIRLSS---HNAFDD 157
|
....*....
gi 1031389505 171 AQILADVYL 179
Cdd:PRK06807 158 CITCAAVYQ 166
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
13-177 |
3.08e-16 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 77.27 E-value: 3.08e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 13 VLDTETTGmnqigAHYEGHKIIEIGAV-----EVINRRLTgnnfhvylkpdrLVDPE----AFGVH--GIADEFLLDKPT 81
Cdd:PRK07883 19 VVDLETTG-----GSPAGDAITEIGAVkvrggEVLGEFAT------------LVNPGrpipPFITVltGITTAMVAGAPP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 82 FADVADEFMDYIRGAELVIHNASFDIGFMDYEFgklnRGIGKTETFCKITDSLALARKMFP--GKRN-SLDALCSRYEID 158
Cdd:PRK07883 82 IEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAA----ARCGYPWPGPPVLCTVRLARRVLPrdEAPNvRLSTLARLFGAT 157
|
170
....*....|....*....
gi 1031389505 159 NSKRtlHGALLDAQILADV 177
Cdd:PRK07883 158 TTPT--HRALDDARATVDV 174
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
8-183 |
3.34e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 75.23 E-value: 3.34e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 8 ITRQIVLDTETTGMnQIgahyEGHKIIEIGAVEVInrrlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVAD 87
Cdd:PRK06309 1 MPALIFYDTETTGT-QI----DKDRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQ 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 88 EFMDYIRG-AELVIHNA-SFDIGFMDYEFgklnRGIGKTETFCKITDSLALARKMFPG-KRNSLDALCSRYEIDNSKRtl 164
Cdd:PRK06309 72 KFIEFCGTdNILVAHNNdAFDFPLLRKEC----RRHGLEPPTLRTIDSLKWAQKYRPDlPKHNLQYLRQVYGFEENQA-- 145
|
170
....*....|....*....
gi 1031389505 165 HGALLDAQILADVYLMMTG 183
Cdd:PRK06309 146 HRALDDVITLHRVFSALVG 164
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
12-179 |
8.29e-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: 8.29e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETtgmnqigAHYEGHKIIEIGAVEVINRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMD 91
Cdd:cd06130 2 VAIDFET-------ANADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 YIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCkitdSLALARKMFPGKRN-SLDALCSRYEIDnskrtL--HGAL 168
Cdd:cd06130 74 FLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLC----TVRLARRVWPLLPNhKLNTVAEHLGIE-----LnhHDAL 144
|
170
....*....|.
gi 1031389505 169 LDAQILADVYL 179
Cdd:cd06130 145 EDARACAEILL 155
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
13-177 |
7.81e-15 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 72.43 E-value: 7.81e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 13 VLDTETTGMNQigahyEGHKIIEIGAVEVINRRLTGNNFHVYLKPDrlVDPEAFGVHGIADEFLLDKPTFADVADEFMDY 92
Cdd:PRK06063 19 VVDVETSGFRP-----GQARIISLAVLGLDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 93 IRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCkitdSLALARKMFPGKRN-SLDALCSRYEIdnSKRTLHGALLDA 171
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMC----TVELARRLGLGLPNlRLETLAAHWGV--PQQRPHDALDDA 165
|
....*.
gi 1031389505 172 QILADV 177
Cdd:PRK06063 166 RVLAGI 171
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
12-185 |
1.53e-13 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 67.23 E-value: 1.53e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQIGAHyeghkIIEIGAVEVI-NRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFM 90
Cdd:PRK09145 32 VALDCETTGLDPRRAE-----IVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 91 DYIRGAELVIHNASFDIGFMD------YEFGKLNRGIgktetfckitDSLAL-ARKMFPGKRN-----SLDALCSRYEID 158
Cdd:PRK09145 107 AFIGNRPLVGYYLEFDVAMLNryvrplLGIPLPNPLI----------EVSALyYDKKERHLPDayidlRFDAILKHLDLP 176
|
170 180
....*....|....*....|....*..
gi 1031389505 159 NSKRtlHGALLDAQILADVYLMMTGGQ 185
Cdd:PRK09145 177 VLGR--HDALNDAIMAALIFLRLRKGD 201
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
13-186 |
4.20e-13 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 66.28 E-value: 4.20e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 13 VLDTETTGMnqigahyEGhKIIEIGAVEVINRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMdy 92
Cdd:PRK07983 4 VIDTETCGL-------QG-GIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY-- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 93 irGAEL-VIHNASFDIGFMDYEFGklnrgigktETFCkitdSLALARKMFPGKRNSLDALcsRYEIDNSKRT-----LHG 166
Cdd:PRK07983 73 --GSEWyVAHNASFDRRVLPEMPG---------EWIC----TMKLARRLWPGIKYSNMAL--YKSRKLNVQTppglhHHR 135
|
170 180
....*....|....*....|..
gi 1031389505 167 ALLDAQILAD--VYLMMTGGQT 186
Cdd:PRK07983 136 ALYDCYITAAllIDIMNTSGWT 157
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
6-171 |
2.84e-12 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 64.66 E-value: 2.84e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 6 TAITRQI--VLDTETTGMNQigahyEGHKIIEIGAV-----EVINRrltgnnFHVYLKPDRLvdPEAFG-VHGIADEFLL 77
Cdd:PRK08517 63 TPIKDQVfcFVDIETNGSKP-----KKHQIIEIGAVkvkngEIIDR------FESFVKAKEV--PEYITeLTGITYEDLE 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 78 DKPTFADVADEFMDYIRGAELVIHNASFDIGFMDYEFGKLNRGIGKTETFCKITdslaLARKMFPGKRNSLDALCSRYEI 157
Cdd:PRK08517 130 NAPSLKEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTID----LAKRTIESPRYGLSFLKELLGI 205
|
170
....*....|....
gi 1031389505 158 DNSkrTLHGALLDA 171
Cdd:PRK08517 206 EIE--VHHRAYADA 217
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
12-178 |
4.82e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 61.00 E-value: 4.82e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQigahyEGHKIIEIGAVevinrRLTGNN----FHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVAD 87
Cdd:PRK06310 10 VCLDCETTGLDV-----KKDRIIEFAAI-----RFTFDEvidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 88 EFMDYIRGAELVI-HNASFDIGFMDYEFGKLnrGIGKTETFCKITDSLALARKMFPGKRNSLDALCSRYEIDNSKRtlHG 166
Cdd:PRK06310 80 QIKGFFKEGDYIVgHSVGFDLQVLSQESERI--GETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--HR 155
|
170
....*....|..
gi 1031389505 167 ALLDAQILADVY 178
Cdd:PRK06310 156 AMKDVEINIKVF 167
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
10-110 |
2.06e-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: 50.87 E-value: 2.06e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTETTGMNQIGAhyeghKIIEIGAVEVINRRLTGNNFHVYLKPDRLVdPEAFGVHGIADEFLLDKP-TFADVADE 88
Cdd:pfam13361 187 NIVVFDVETTGLDTTED-----EIIQIAAIKLNKKGVVIESFERFLRLKKPV-GDSLQVHGFSDEFLQENGeTPAEALRD 260
|
90 100
....*....|....*....|...
gi 1031389505 89 FMDYIRG-AELVIHNASFDIGFM 110
Cdd:pfam13361 261 FLEKLENlRELYSILREYDDIEE 283
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
12-111 |
2.32e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 50.36 E-value: 2.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQigahyEGHKIIEIGAVEViNRRLTGN------NFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADV 85
Cdd:PRK09182 40 VILDTETTGLDP-----RKDEIIEIGMVAF-EYDDDGRigdvldTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA 113
|
90 100
....*....|....*....|....*..
gi 1031389505 86 ADEFMDyirGAELVI-HNASFDIGFMD 111
Cdd:PRK09182 114 VDALIA---PADLIIaHNAGFDRPFLE 137
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
12-181 |
2.77e-07 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 49.97 E-value: 2.77e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQIGAHYEGHKIIEIGAV-EVINRRltgnnfhvylkpDRLVDP------EAFGVHGIADEFL-LDKPTFA 83
Cdd:PRK07942 9 AAFDLETTGVDPETARIVTAALVVVDADgEVVESR------------EWLADPgveipeEASAVHGITTEYArAHGRPAA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 84 DVADEFMDYIR-----GAELVIHNASFDIGFMDYEFGKLnrGIGKTETFCKItDSLALARKMFP---GKRNsLDALCSRY 155
Cdd:PRK07942 77 EVLAEIADALReawarGVPVVVFNAPYDLTVLDRELRRH--GLPSLVPGPVI-DPYVIDKAVDRyrkGKRT-LTALCEHY 152
|
170 180
....*....|....*....|....*...
gi 1031389505 156 EI--DNSkrtlHGALLDAQILADVYLMM 181
Cdd:PRK07942 153 GVrlDNA----HEATADALAAARVAWAL 176
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
12-177 |
1.05e-06 |
|
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: 47.60 E-value: 1.05e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNQIGAHYEGHKIIEIGAVeVINRRLTGN--NFHVYLKP---DRLVDpeaF--GVHGIADEFLLDKPTFAD 84
Cdd:cd06133 2 LVIDFEATCWEGNSKPDYPNEIIEIGAV-LVDVKTKEIidTFSSYVKPvinPKLSD---FctELTGITQEDVDNAPSFPE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 85 VADEFMDYIRGaelvihnasfDIGFMDYEFGKL-NRGIGKTETFCKITDSLALARKMF-----------PGKRNSLDALC 152
Cdd:cd06133 78 VLKEFLEWLGK----------NGKYAFVTWGDWdLKDLLQNQCKYKIINLPPFFRQWIdlkkefakfygLKKRTGLSKAL 147
|
170 180
....*....|....*....|....*
gi 1031389505 153 SRYEIDNSKRTlHGALLDAQILADV 177
Cdd:cd06133 148 EYLGLEFEGRH-HRGLDDARNIARI 171
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
14-111 |
4.57e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 46.46 E-value: 4.57e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 14 LDTETTGMNQigahyEGHKIIEIGAVEV-INRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFADVADEFMDY 92
Cdd:PRK09146 52 LDFETTGLDA-----EQDAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126
|
90
....*....|....*....
gi 1031389505 93 IRGAELVIHNASFDIGFMD 111
Cdd:PRK09146 127 LAGKVVVVHYRRIERDFLD 145
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
36-108 |
1.13e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 45.54 E-value: 1.13e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1031389505 36 IGAVEVINRRLTGNNFHVyLKPDRLV-DPEAFGVHGIADEFLLDKPTFADVADEFMDYIRGAELVIHNASFDIG 108
Cdd:PRK06195 21 IGIVVVKDGEIVEKVHYL-IKPKEMRfMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDIS 93
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
25-139 |
7.63e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 43.28 E-value: 7.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 25 GAHYEGHKIIEIGAVEVINRRLTGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFADVADEFMDYIRGAELVIHNAS 104
Cdd:PRK05601 57 GIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGE--DPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAP 134
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1031389505 105 FDIGFMDYEF--------------------GKLNRG---IGKTETFCKITDSLALARK 139
Cdd:PRK05601 135 RTWGFIVSEAkramnaaaranrnrnrgnrrGGRGRRrqrVGHIPKPVVIVDTLATARR 192
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
10-183 |
6.85e-04 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 39.46 E-value: 6.85e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 10 RQIVLDTEttgMNQI-GAHYEGHK--IIEIGAVEVINRRLTGNNFHVYLKPDR--LVDPEAFGVHGIADEFLLDKPTFAD 84
Cdd:COG5018 3 KYLVIDLE---ATCWdGKPPPGFPmeIIEIGAVKVDENGEIIDEFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 85 VADEFMDYIRGAELVIhnASFdiGFMD--------------YEFGKLNRGIgKTEtfckitdsLALARKMfpGKRNSLDA 150
Cdd:COG5018 80 AIEDFKKWIGSEDYIL--CSW--GDYDrkqlerncrfhgvpYPFGDRHINL-KKL--------FALYFGL--KKRIGLKK 144
|
170 180 190
....*....|....*....|....*....|...
gi 1031389505 151 LCSRYEIDNsKRTLHGALLDAQILADVYLMMTG 183
Cdd:COG5018 145 ALELLGLEF-EGTHHRALDDARNTAKLFKKILG 176
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
4-179 |
1.71e-03 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 39.28 E-value: 1.71e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 4 MSTAITRQ-IVLDTETTGmnqigAHYEGhKIIEIGAV-----EVINRRLTGNNFHvylkpdrlvdpEAFGVH-----GIA 72
Cdd:PRK07246 1 MTQKKLRKyAVVDLEATG-----AGPNA-SIIQVGIViieggEIIDSYTTDVNPH-----------EPLDEHikhltGIT 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 73 DEFLLDKPTFADVADEFMDYIRGAELVIHNASFDIG------FMD-YEFgkLNRGIgktetfckitDSLALARKMFPG-K 144
Cdd:PRK07246 64 DQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANllaealFLEgYEL--RTPRV----------DTVELAQVFFPTlE 131
|
170 180 190
....*....|....*....|....*....|....*
gi 1031389505 145 RNSLDALCSRYEIDNSKRtlHGALLDAQILADVYL 179
Cdd:PRK07246 132 KYSLSHLSRELNIDLADA--HTAIADARATAELFL 164
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
12-180 |
5.15e-03 |
|
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Pssm-ID: 176654 [Multi-domain] Cd Length: 178 Bit Score: 36.74 E-value: 5.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 12 IVLDTETTGMNqigaHYEGhkiiEIGAVEVinrrLTGNNFHvylkpdrLVDPEAfgvhgiadefLLDKPTFADVadeFMD 91
Cdd:cd06142 15 IAVDTEFMRLN----TYYP----RLCLIQI----STGGEVY-------LIDPLA----------IGDLSPLKEL---LAD 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1031389505 92 yiRGAELVIHNASFDIGFMDYEFGKLNRGIgktetFC-KItdSLALARKmfpGKRNSLDALCSRY---EIDNSKRT---L 164
Cdd:cd06142 63 --PNIVKVFHAAREDLELLKRDFGILPQNL-----FDtQI--AARLLGL---GDSVGLAALVEELlgvELDKGEQRsdwS 130
|
170 180
....*....|....*....|
gi 1031389505 165 HGALLDAQI---LADV-YLM 180
Cdd:cd06142 131 KRPLTDEQLeyaALDVrYLL 150
|
|
| |
