|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-246 |
0e+00 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 497.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 6 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 86 ADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 166 GALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEELAAHEARLDLVEKKGGSCLWR 245
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1014579970 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 |
2.65e-116 |
|
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: 331.67 E-value: 2.65e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 170 DAQILAEVYLAMTGGQTSmAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEELAAHEARLDLVEKKG 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 |
3.96e-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: 313.70 E-value: 3.96e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 91 DYIRGAELVIHNAAFDIGFMDYEFSLLkRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1014579970 171 AQILAEVYLAMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
3.56e-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: 204.64 E-value: 3.56e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1014579970 169 LDAQILAEVYLAMTG 183
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
10-183 |
2.27e-47 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 154.77 E-value: 2.27e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHN-AAFDIGFMDYEFsllKRDIPKTNTFCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1014579970 168 LLDAQILAEVYLAMTG 183
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
12-178 |
3.25e-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: 3.25e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFAEVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 89 FMDYIR-GAELVIHNAAFDIGFMDYEFS-LLKRDIPKTNTFCKVTDSLAVARKMFPgkRNSLDALCARYEIDNSKRtLHG 166
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKrFLKKPMPKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 1014579970 167 ALLDAQILAEVY 178
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
6-246 |
0e+00 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 497.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 6 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEV 85
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 86 ADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLH 165
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 166 GALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEELAAHEARLDLVEKKGGSCLWR 245
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 1014579970 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 |
2.65e-116 |
|
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: 331.67 E-value: 2.65e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALL 169
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 170 DAQILAEVYLAMTGGQTSmAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEELAAHEARLDLVEKKG 239
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQES-LLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
9-228 |
1.61e-110 |
|
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: 316.70 E-value: 1.61e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 9 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADE 88
Cdd:TIGR00573 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 89 FMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGAL 168
Cdd:TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 169 LDAQILAEVYLAMTGGQTSMAfamEGETQQQQGEATIQRIVRQASKLRVVFATDEELAAH 228
Cdd:TIGR00573 161 ADAFILAKLYLVMTGKQTKYG---ENEGQQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
11-182 |
3.96e-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: 313.70 E-value: 3.96e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 11 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 90
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 91 DYIRGAELVIHNAAFDIGFMDYEFSLLkRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLD 170
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 1014579970 171 AQILAEVYLAMT 182
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
10-183 |
3.56e-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: 204.64 E-value: 3.56e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtlHGAL 168
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 1014579970 169 LDAQILAEVYLAMTG 183
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
10-183 |
2.27e-47 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 154.77 E-value: 2.27e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHN-AAFDIGFMDYEFsllKRDIPKTNTFCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRTlHGA 167
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 1014579970 168 LLDAQILAEVYLAMTG 183
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
12-181 |
5.01e-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: 5.01e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 91
Cdd:COG2176 11 VVFDLETTGLS-----PKKDEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 92 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPktntfCKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGALLD 170
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFD-----NPVLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGD 157
|
170
....*....|.
gi 1014579970 171 AQILAEVYLAM 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 |
2.15e-45 |
|
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: 149.37 E-value: 2.15e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 91
Cdd:cd06127 1 VVFDTETTGLD-----PKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 92 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPGKRNSL--DALCARYEIDNSKRtlHGALL 169
Cdd:cd06127 76 FLGGRVLVAHNASFDLRFLNRELRRLGGPPLP----NPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALA 149
|
170
....*....|
gi 1014579970 170 DAQILAEVYL 179
Cdd:cd06127 150 DALATAELLL 159
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
12-178 |
3.25e-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: 3.25e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFAEVADE 88
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 89 FMDYIR-GAELVIHNAAFDIGFMDYEFS-LLKRDIPKTNTFCKVTDSLAVARKMFPgkRNSLDALCARYEIDNSKRtLHG 166
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKrFLKKPMPKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 1014579970 167 ALLDAQILAEVY 178
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
13-181 |
1.57e-25 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 104.92 E-value: 1.57e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 13 VLDTETTGMNqigAHYegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 92
Cdd:PRK00448 423 VFDVETTGLS---AVY--DEIIEIGAVKIKNGEII-DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEF 496
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 93 IRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtNTfckVTDSLAVARKMFPG-KRNSLDALCARYEI--DNSkrtlHGALL 169
Cdd:PRK00448 497 CGDSILVAHNASFDVGFINTNYEKLGLEKIK-NP---VIDTLELSRFLYPElKSHRLNTLAKKFGVelEHH----HRADY 568
|
170
....*....|..
gi 1014579970 170 DAQILAEVYLAM 181
Cdd:PRK00448 569 DAEATAYLLIKF 580
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
12-180 |
1.77e-19 |
|
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: 81.79 E-value: 1.77e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETtgmnqigAHYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 91
Cdd:cd06130 2 VAIDFET-------ANADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 92 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCkvtdSLAVARKMFPGKRN-SLDALCARYEIDnskrtL--HGAL 168
Cdd:cd06130 74 FLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLC----TVRLARRVWPLLPNhKLNTVAEHLGIE-----LnhHDAL 144
|
170
....*....|..
gi 1014579970 169 LDAQILAEVYLA 180
Cdd:cd06130 145 EDARACAEILLA 156
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
12-178 |
1.92e-19 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 83.95 E-value: 1.92e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 91
Cdd:PRK07740 62 VVFDLETTGFS----PQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 92 YIRGAELVIHNAAFDIGFMDYEFSLLKRdIPKTNTFckvTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGALLD 170
Cdd:PRK07740 138 FIGAGVLVAHHAGHDKAFLRHALWRTYR-QPFTHRL---IDTMFLTKLLAHERDFpTLDDALAYYGIPIPRR--HHALGD 211
|
....*...
gi 1014579970 171 AQILAEVY 178
Cdd:PRK07740 212 ALMTAKLW 219
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
12-179 |
9.04e-19 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 83.32 E-value: 9.04e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQIGahyegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 91
Cdd:PRK06807 11 VVIDFETTGFNPYN-----DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 92 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTntfcKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKrtlHGALLD 170
Cdd:PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN----KVIDTVFLAKKYMKHAPNhKLETLKRMLGIRLSS---HNAFDD 157
|
....*....
gi 1014579970 171 AQILAEVYL 179
Cdd:PRK06807 158 CITCAAVYQ 166
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
10-181 |
2.40e-18 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 83.85 E-value: 2.40e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGmNQIGahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 89
Cdd:PRK08074 4 RFVVVDLETTG-NSPK---KGDKIIQIAAVVVEDGEIL-ERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 90 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGAL 168
Cdd:PRK08074 79 VELLEGAYFVAHNVHFDLNFLNEELERAGYTEIH----CPKLDTVELARILLPTAESyKLRDLSEELGLEHDQP--HRAD 152
|
170
....*....|...
gi 1014579970 169 LDAQILAEVYLAM 181
Cdd:PRK08074 153 SDAEVTAELFLQL 165
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
13-177 |
1.19e-17 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 80.13 E-value: 1.19e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 13 VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDrlVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 92
Cdd:PRK06063 19 VVDVETSGFRP-----GQARIISLAVLGLDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 93 IRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVtdslAVARKMFPGKRN-SLDALCARYEIdnSKRTLHGALLDA 171
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTV----ELARRLGLGLPNlRLETLAAHWGV--PQQRPHDALDDA 165
|
....*.
gi 1014579970 172 QILAEV 177
Cdd:PRK06063 166 RVLAGI 171
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
8-183 |
4.33e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 77.54 E-value: 4.33e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 8 ITRQIVLDTETTGMnQIgahyEGHKIIEIGAVEVVnrrlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVAD 87
Cdd:PRK06309 1 MPALIFYDTETTGT-QI----DKDRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQ 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 88 EFMDYIRG-AELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFckvtDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtl 164
Cdd:PRK06309 72 KFIEFCGTdNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTI----DSLKWAQKYRPDlPKHNLQYLRQVYGFEENQA-- 145
|
170
....*....|....*....
gi 1014579970 165 HGALLDAQILAEVYLAMTG 183
Cdd:PRK06309 146 HRALDDVITLHRVFSALVG 164
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
13-180 |
1.70e-16 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 78.04 E-value: 1.70e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 13 VLDTETTGmnqigAHYEGHKIIEIGAV-----EVVNRRLTgnnfhvylkpdrLVDPE----AFGVH--GIADEFLLDKPT 81
Cdd:PRK07883 19 VVDLETTG-----GSPAGDAITEIGAVkvrggEVLGEFAT------------LVNPGrpipPFITVltGITTAMVAGAPP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 82 FAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTntfcKVTDSLAVARKMFPG---KRNSLDALCARYEID 158
Cdd:PRK07883 82 IEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGP----PVLCTVRLARRVLPRdeaPNVRLSTLARLFGAT 157
|
170 180
....*....|....*....|..
gi 1014579970 159 NSKRtlHGALLDAQILAEVYLA 180
Cdd:PRK07883 158 TTPT--HRALDDARATVDVLHG 177
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
12-185 |
3.16e-15 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 71.86 E-value: 3.16e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQIGAHyeghkIIEIGAVEVV-NRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 90
Cdd:PRK09145 32 VALDCETTGLDPRRAE-----IVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 91 DYIRGAELVIHNAAFDIGFMD-YEFSLLKRDIPktNTFCKVTdSLAVARKM--FPGKRN--SLDALCARYEIDNSKRtlH 165
Cdd:PRK09145 107 AFIGNRPLVGYYLEFDVAMLNrYVRPLLGIPLP--NPLIEVS-ALYYDKKErhLPDAYIdlRFDAILKHLDLPVLGR--H 181
|
170 180
....*....|....*....|
gi 1014579970 166 GALLDAQILAEVYLAMTGGQ 185
Cdd:PRK09145 182 DALNDAIMAALIFLRLRKGD 201
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
13-181 |
8.97e-13 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 65.51 E-value: 8.97e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 13 VLDTETTGMnqigahyEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMdy 92
Cdd:PRK07983 4 VIDTETCGL-------QG-GIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY-- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 93 irGAEL-VIHNAAFDigfmdyefsllKRDIPKTNT--FCKVTdslaVARKMFPGKRNSLDALcaRYEIDNSKRT-----L 164
Cdd:PRK07983 73 --GSEWyVAHNASFD-----------RRVLPEMPGewICTMK----LARRLWPGIKYSNMAL--YKSRKLNVQTppglhH 133
|
170
....*....|....*..
gi 1014579970 165 HGALLDAQILAEVYLAM 181
Cdd:PRK07983 134 HRALYDCYITAALLIDI 150
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
12-178 |
4.96e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 61.00 E-value: 4.96e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQigahyEGHKIIEIGAVevvnrRLTGNN----FHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVAD 87
Cdd:PRK06310 10 VCLDCETTGLDV-----KKDRIIEFAAI-----RFTFDEvidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 88 EFMDYIRGAELVI-HNAAFDIGFMDYEFSLLKRD-IPKTNTFckvTDSLAVARKMFPGKRNSLDALCARYEIDNSKRtlH 165
Cdd:PRK06310 80 QIKGFFKEGDYIVgHSVGFDLQVLSQESERIGETfLSKHYYI---IDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--H 154
|
170
....*....|...
gi 1014579970 166 GALLDAQILAEVY 178
Cdd:PRK06310 155 RAMKDVEINIKVF 167
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
6-178 |
1.72e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 59.27 E-value: 1.72e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 6 TAITRQI--VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLvdPEAFG-VHGIADEFLLDKPTF 82
Cdd:PRK08517 63 TPIKDQVfcFVDIETNGSKP-----KKHQIIEIGAVKVKNGEII-DRFESFVKAKEV--PEYITeLTGITYEDLENAPSL 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 83 AEVADEFMDYIRGAELVIHNAAFDIGFMDYEFS------LLKRDIpktntfckvtDSLAVARKMFPGKRNSLDALCARYE 156
Cdd:PRK08517 135 KEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEeiglgpLLNRKL----------CTIDLAKRTIESPRYGLSFLKELLG 204
|
170 180
....*....|....*....|..
gi 1014579970 157 IDNSkrTLHGALLDAQILAEVY 178
Cdd:PRK08517 205 IEIE--VHHRAYADALAAYEIF 224
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
12-181 |
8.54e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 51.52 E-value: 8.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTgnnfhvylkpdRLVDP------EAFGVHGIADEFLLDK-----P 80
Cdd:PRK07942 9 AAFDLETTGVDPETARIVTAALVVVDADGEVVESRE-----------WLADPgveipeEASAVHGITTEYARAHgrpaaE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 81 TFAEVADEFMDYIR-GAELVIHNAAFDIGFMDYEfsLLKRDIPKTNTFcKVTDSLAVARKMFP---GKRNsLDALCARYE 156
Cdd:PRK07942 78 VLAEIADALREAWArGVPVVVFNAPYDLTVLDRE--LRRHGLPSLVPG-PVIDPYVIDKAVDRyrkGKRT-LTALCEHYG 153
|
170 180
....*....|....*....|....*..
gi 1014579970 157 I--DNSkrtlHGALLDAQILAEVYLAM 181
Cdd:PRK07942 154 VrlDNA----HEATADALAAARVAWAL 176
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
10-94 |
1.76e-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: 51.25 E-value: 1.76e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTETTGMNQIGAhyeghKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVdPEAFGVHGIADEFLLDKP-TFAEVADE 88
Cdd:pfam13361 187 NIVVFDVETTGLDTTED-----EIIQIAAIKLNKKGVVIESFERFLRLKKPV-GDSLQVHGFSDEFLQENGeTPAEALRD 260
|
....*.
gi 1014579970 89 FMDYIR 94
Cdd:pfam13361 261 FLEKLE 266
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
12-111 |
2.41e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 50.36 E-value: 2.41e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQigahyEGHKIIEIGAV-----------EVVNRrltgnnFHVYLKPDRLVDPEAFGVHGIADEFLLDKP 80
Cdd:PRK09182 40 VILDTETTGLDP-----RKDEIIEIGMVafeydddgrigDVLDT------FGGLQQPSRPIPPEITRLTGITDEMVAGQT 108
|
90 100 110
....*....|....*....|....*....|..
gi 1014579970 81 TFAEVADEFMDyirGAELVI-HNAAFDIGFMD 111
Cdd:PRK09182 109 IDPAAVDALIA---PADLIIaHNAGFDRPFLE 137
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
36-146 |
3.50e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 50.16 E-value: 3.50e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 36 IGAVEVVNRRLTGNNFHVyLKPDRLV-DPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEF 114
Cdd:PRK06195 21 IGIVVVKDGEIVEKVHYL-IKPKEMRfMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTL 99
|
90 100 110
....*....|....*....|....*....|..
gi 1014579970 115 SLLKRDIPKTNTFCkvtdSLAVARKMFPGKRN 146
Cdd:PRK06195 100 ELYNIPMPSFEYIC----TMKLAKNFYSNIDN 127
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
12-181 |
4.37e-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: 4.37e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 12 IVLDTETTGMNQIGAHYEGHKIIEIGAVEV-VNRRLTGNNFHVYLKP---DRLVDpeaF--GVHGIADEFLLDKPTFAEV 85
Cdd:cd06133 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVdVKTKEIIDTFSSYVKPvinPKLSD---FctELTGITQEDVDNAPSFPEV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 86 ADEFMDYIRGAElvihNAAF------DIGFMDYEFSLLKRdIPKTNTFCKVTD-SLAVARKMFPGKRNSLDALCARYEID 158
Cdd:cd06133 79 LKEFLEWLGKNG----KYAFvtwgdwDLKDLLQNQCKYKI-INLPPFFRQWIDlKKEFAKFYGLKKRTGLSKALEYLGLE 153
|
170 180
....*....|....*....|...
gi 1014579970 159 NSKRTlHGALLDAQILAEVYLAM 181
Cdd:cd06133 154 FEGRH-HRGLDDARNIARILKRL 175
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
14-111 |
2.81e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 46.84 E-value: 2.81e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 14 LDTETTGMNQigahyEGHKIIEIGAVEV-VNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 92
Cdd:PRK09146 52 LDFETTGLDA-----EQDAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126
|
90
....*....|....*....
gi 1014579970 93 IRGAELVIHNAAFDIGFMD 111
Cdd:PRK09146 127 LAGKVVVVHYRRIERDFLD 145
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
10-183 |
5.23e-05 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 42.54 E-value: 5.23e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 10 RQIVLDTEttgMNQI-GAHYEGHK--IIEIGAVEV-VNRRLTGnNFHVYLKPDR--LVDPEAFGVHGIADEFLLDKPTFA 83
Cdd:COG5018 3 KYLVIDLE---ATCWdGKPPPGFPmeIIEIGAVKVdENGEIID-EFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 84 EVADEFMDYIRGAELVIhnaafdIGFMDYEFSLLKRDIpktnTFCKVTDSL-----------AVARKMfpGKRNSLDALC 152
Cdd:COG5018 79 EAIEDFKKWIGSEDYIL------CSWGDYDRKQLERNC----RFHGVPYPFgdrhinlkklfALYFGL--KKRIGLKKAL 146
|
170 180 190
....*....|....*....|....*....|.
gi 1014579970 153 ARYEIDNsKRTLHGALLDAQILAEVYLAMTG 183
Cdd:COG5018 147 ELLGLEF-EGTHHRALDDARNTAKLFKKILG 176
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
25-125 |
5.30e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 43.66 E-value: 5.30e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 25 GAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAA 104
Cdd:PRK05601 57 GIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGE--DPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAP 134
|
90 100
....*....|....*....|.
gi 1014579970 105 FDIGFMDYEFSLLKRDIPKTN 125
Cdd:PRK05601 135 RTWGFIVSEAKRAMNAAARAN 155
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
4-179 |
4.84e-04 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 41.21 E-value: 4.84e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 4 MSTAITRQ-IVLDTETTGmnqigAHYEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTF 82
Cdd:PRK07246 1 MTQKKLRKyAVVDLEATG-----AGPNA-SIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDF 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1014579970 83 AEVADEFMDYIRGAELVIHNAAFDIG------FMD-YEFSllkrdIPKtntfckvTDSLAVARKMFPG-KRNSLDALCAR 154
Cdd:PRK07246 74 SQVARHIYDLIEDCIFVAHNVKFDANllaealFLEgYELR-----TPR-------VDTVELAQVFFPTlEKYSLSHLSRE 141
|
170 180
....*....|....*....|....*
gi 1014579970 155 YEIDNSKRtlHGALLDAQILAEVYL 179
Cdd:PRK07246 142 LNIDLADA--HTAIADARATAELFL 164
|
|
| |
