|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
3-243 |
0e+00 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 496.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 3 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEV 82
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 83 ADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLH 162
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 163 GALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKGGSCLWR 242
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 16128202 243 A 243
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
7-236 |
7.13e-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: 330.51 E-value: 7.13e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALL 166
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 167 DAQILAEVYLAMTGGQTSmAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKG 236
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 ... |
8-179 |
3.89e-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: 3.89e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 8 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 87
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 88 DYIRGAELVIHNAAFDIGFMDYEFSLLkRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLD 167
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 16128202 168 AQILAEVYLAMT 179
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
7-180 |
2.60e-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: 205.03 E-value: 2.60e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtlHGAL 165
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 16128202 166 LDAQILAEVYLAMTG 180
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
7-180 |
1.77e-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: 1.77e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHN-AAFDIGFMDYEFsllKRDIPKTNTFCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRTlHGA 164
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 16128202 165 LLDAQILAEVYLAMTG 180
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
9-175 |
2.96e-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: 2.96e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFAEVADE 85
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 86 FMDYIR-GAELVIHNAAFDIGFMDYEFS-LLKRDIPKTNTFCKVTDSLAVARKMFPgkRNSLDALCARYEIDNSKRtLHG 163
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKrFLKKPMPKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 16128202 164 ALLDAQILAEVY 175
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
3-243 |
0e+00 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 496.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 3 TAITRQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEV 82
Cdd:PRK05711 1 TAIMRQIVLDTETTGLNQRE----GHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 83 ADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLH 162
Cdd:PRK05711 77 ADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLH 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 163 GALLDAQILAEVYLAMTGGQTSMAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKGGSCLWR 242
Cdd:PRK05711 157 GALLDAEILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
.
gi 16128202 243 A 243
Cdd:PRK05711 237 K 237
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
7-236 |
7.13e-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: 330.51 E-value: 7.13e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNQIGahyeGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:TIGR01406 1 RQIILDTETTGLDPKG----GHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALL 166
Cdd:TIGR01406 77 LDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALL 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 167 DAQILAEVYLAMTGGQTSmAFAMEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAHEARLDLVQKKG 236
Cdd:TIGR01406 157 DAHLLAEVYLALTGGQES-LLELAESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
6-225 |
2.05e-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: 316.31 E-value: 2.05e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 6 TRQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADE 85
Cdd:TIGR00573 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 86 FMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGAL 165
Cdd:TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 166 LDAQILAEVYLAMTGGQTSMAfamEGETQQQQGEATIQRIVRQASKLRVVFATDEEIAAH 225
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 ... |
8-179 |
3.89e-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: 3.89e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 8 QIVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 87
Cdd:cd06131 1 QIVLDTETTGLD----PREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 88 DYIRGAELVIHNAAFDIGFMDYEFSLLkRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLD 167
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLL-GLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLD 155
|
170
....*....|..
gi 16128202 168 AQILAEVYLAMT 179
Cdd:cd06131 156 AELLAEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
7-180 |
2.60e-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: 205.03 E-value: 2.60e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:COG0847 1 RFVVLDTETTGLD-----PAKDRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtlHGAL 165
Cdd:COG0847 75 LEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPP----FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRAL 148
|
170
....*....|....*
gi 16128202 166 LDAQILAEVYLAMTG 180
Cdd:COG0847 149 ADAEATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
7-180 |
1.77e-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: 1.77e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:smart00479 1 TLVVIDCETTGLDP-----GKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEEL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHN-AAFDIGFMDYEFsllKRDIPKTNTFCKVTDSLAVARKMFPG-KRNSLDALCARYEIDNSKRTlHGA 164
Cdd:smart00479 75 LEFLRGRILVAGNsAHFDLRFLKLEH---PRLGIKQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRA 150
|
170
....*....|....*.
gi 16128202 165 LLDAQILAEVYLAMTG 180
Cdd:smart00479 151 LDDARATAKLFKKLLE 166
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
9-178 |
3.83e-46 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 151.84 E-value: 3.83e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 88
Cdd:COG2176 11 VVFDLETTGLS-----PKKDEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 89 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPktntfCKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGALLD 167
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFD-----NPVLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGD 157
|
170
....*....|.
gi 16128202 168 AQILAEVYLAM 178
Cdd:COG2176 158 AEATAELFLKL 168
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
9-176 |
1.98e-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: 1.98e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNqigahYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 88
Cdd:cd06127 1 VVFDTETTGLD-----PKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 89 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPGKRNSL--DALCARYEIDNSKRtlHGALL 166
Cdd:cd06127 76 FLGGRVLVAHNASFDLRFLNRELRRLGGPPLP----NPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALA 149
|
170
....*....|
gi 16128202 167 DAQILAEVYL 176
Cdd:cd06127 150 DALATAELLL 159
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
9-175 |
2.96e-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: 2.96e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQigahyEGHKIIEIGAVEVVNRRL-TGNNFHVYLKPDRL--VDPEAFGVHGIADEFLLDKPTFAEVADE 85
Cdd:pfam00929 1 VVIDLETTGLDP-----EKDEIIEIAAVVIDGGENeIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 86 FMDYIR-GAELVIHNAAFDIGFMDYEFS-LLKRDIPKTNTFCKVTDSLAVARKMFPgkRNSLDALCARYEIDNSKRtLHG 163
Cdd:pfam00929 76 FLEFLRkGNLLVAHNASFDVGFLRYDDKrFLKKPMPKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHIGR-AHR 152
|
170
....*....|..
gi 16128202 164 ALLDAQILAEVY 175
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
10-178 |
1.71e-25 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 104.53 E-value: 1.71e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 10 VLDTETTGMNqigAHYegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 89
Cdd:PRK00448 423 VFDVETTGLS---AVY--DEIIEIGAVKIKNGEII-DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEF 496
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 90 IRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtNTfckVTDSLAVARKMFPG-KRNSLDALCARYEI--DNSkrtlHGALL 166
Cdd:PRK00448 497 CGDSILVAHNASFDVGFINTNYEKLGLEKIK-NP---VIDTLELSRFLYPElKSHRLNTLAKKFGVelEHH----HRADY 568
|
170
....*....|..
gi 16128202 167 DAQILAEVYLAM 178
Cdd:PRK00448 569 DAEATAYLLIKF 580
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
9-175 |
1.48e-19 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 84.34 E-value: 1.48e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNqigaHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 88
Cdd:PRK07740 62 VVFDLETTGFS----PQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 89 YIRGAELVIHNAAFDIGFMDYEFSLLKRdIPKTNTFckvTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGALLD 167
Cdd:PRK07740 138 FIGAGVLVAHHAGHDKAFLRHALWRTYR-QPFTHRL---IDTMFLTKLLAHERDFpTLDDALAYYGIPIPRR--HHALGD 211
|
....*...
gi 16128202 168 AQILAEVY 175
Cdd:PRK07740 212 ALMTAKLW 219
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
9-177 |
1.70e-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: 1.70e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETtgmnqigAHYEGHKIIEIGAVEVVNRRLTGNnFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 88
Cdd:cd06130 2 VAIDFET-------ANADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 89 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCkvtdSLAVARKMFPGKRN-SLDALCARYEIDnskrtL--HGAL 165
Cdd:cd06130 74 FLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLC----TVRLARRVWPLLPNhKLNTVAEHLGIE-----LnhHDAL 144
|
170
....*....|..
gi 16128202 166 LDAQILAEVYLA 177
Cdd:cd06130 145 EDARACAEILLA 156
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
9-176 |
8.40e-19 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 83.32 E-value: 8.40e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQIGahyegHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMD 88
Cdd:PRK06807 11 VVIDFETTGFNPYN-----DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 89 YIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTntfcKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKrtlHGALLD 167
Cdd:PRK06807 85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN----KVIDTVFLAKKYMKHAPNhKLETLKRMLGIRLSS---HNAFDD 157
|
....*....
gi 16128202 168 AQILAEVYL 176
Cdd:PRK06807 158 CITCAAVYQ 166
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
7-178 |
2.08e-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: 2.08e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGmNQIGahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEF 86
Cdd:PRK08074 4 RFVVVDLETTG-NSPK---KGDKIIQIAAVVVEDGEIL-ERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 87 MDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKtntfCKVTDSLAVARKMFPGKRN-SLDALCARYEIDNSKRtlHGAL 165
Cdd:PRK08074 79 VELLEGAYFVAHNVHFDLNFLNEELERAGYTEIH----CPKLDTVELARILLPTAESyKLRDLSEELGLEHDQP--HRAD 152
|
170
....*....|...
gi 16128202 166 LDAQILAEVYLAM 178
Cdd:PRK08074 153 SDAEVTAELFLQL 165
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
10-174 |
8.98e-18 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 80.52 E-value: 8.98e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 10 VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDrlVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 89
Cdd:PRK06063 19 VVDVETSGFRP-----GQARIISLAVLGLDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 90 IRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVtdslAVARKMFPGKRN-SLDALCARYEIdnSKRTLHGALLDA 168
Cdd:PRK06063 92 LRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTV----ELARRLGLGLPNlRLETLAAHWGV--PQQRPHDALDDA 165
|
....*.
gi 16128202 169 QILAEV 174
Cdd:PRK06063 166 RVLAGI 171
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
5-180 |
4.43e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 77.54 E-value: 4.43e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 5 ITRQIVLDTETTGMnQIgahyEGHKIIEIGAVEVVnrrlTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVAD 84
Cdd:PRK06309 1 MPALIFYDTETTGT-QI----DKDRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQ 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 85 EFMDYIRG-AELVIHNA-AFDIGFMDYEFSLLKRDIPKTNTFckvtDSLAVARKMFPG-KRNSLDALCARYEIDNSKRtl 161
Cdd:PRK06309 72 KFIEFCGTdNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTI----DSLKWAQKYRPDlPKHNLQYLRQVYGFEENQA-- 145
|
170
....*....|....*....
gi 16128202 162 HGALLDAQILAEVYLAMTG 180
Cdd:PRK06309 146 HRALDDVITLHRVFSALVG 164
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
10-177 |
1.10e-16 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 78.81 E-value: 1.10e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 10 VLDTETTGmnqigAHYEGHKIIEIGAV-----EVVNRRLTgnnfhvylkpdrLVDPE----AFGVH--GIADEFLLDKPT 78
Cdd:PRK07883 19 VVDLETTG-----GSPAGDAITEIGAVkvrggEVLGEFAT------------LVNPGrpipPFITVltGITTAMVAGAPP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 79 FAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTntfcKVTDSLAVARKMFPG---KRNSLDALCARYEID 155
Cdd:PRK07883 82 IEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGP----PVLCTVRLARRVLPRdeaPNVRLSTLARLFGAT 157
|
170 180
....*....|....*....|..
gi 16128202 156 NSKRtlHGALLDAQILAEVYLA 177
Cdd:PRK07883 158 TTPT--HRALDDARATVDVLHG 177
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
9-182 |
3.06e-15 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 71.86 E-value: 3.06e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQIGAHyeghkIIEIGAVEVV-NRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFM 87
Cdd:PRK09145 32 VALDCETTGLDPRRAE-----IVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 88 DYIRGAELVIHNAAFDIGFMD-YEFSLLKRDIPktNTFCKVTdSLAVARKM--FPGKRN--SLDALCARYEIDNSKRtlH 162
Cdd:PRK09145 107 AFIGNRPLVGYYLEFDVAMLNrYVRPLLGIPLP--NPLIEVS-ALYYDKKErhLPDAYIdlRFDAILKHLDLPVLGR--H 181
|
170 180
....*....|....*....|
gi 16128202 163 GALLDAQILAEVYLAMTGGQ 182
Cdd:PRK09145 182 DALNDAIMAALIFLRLRKGD 201
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
10-178 |
8.56e-13 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 65.51 E-value: 8.56e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 10 VLDTETTGMnqigahyEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMdy 89
Cdd:PRK07983 4 VIDTETCGL-------QG-GIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY-- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 90 irGAEL-VIHNAAFDigfmdyefsllKRDIPKTNT--FCKVTdslaVARKMFPGKRNSLDALcaRYEIDNSKRT-----L 161
Cdd:PRK07983 73 --GSEWyVAHNASFD-----------RRVLPEMPGewICTMK----LARRLWPGIKYSNMAL--YKSRKLNVQTppglhH 133
|
170
....*....|....*..
gi 16128202 162 HGALLDAQILAEVYLAM 178
Cdd:PRK07983 134 HRALYDCYITAALLIDI 150
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
9-175 |
5.04e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 61.00 E-value: 5.04e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQigahyEGHKIIEIGAVevvnrRLTGNN----FHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVAD 84
Cdd:PRK06310 10 VCLDCETTGLDV-----KKDRIIEFAAI-----RFTFDEvidsVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 85 EFMDYIRGAELVI-HNAAFDIGFMDYEFSLLKRD-IPKTNTFckvTDSLAVARKMFPGKRNSLDALCARYEIDNSKRtlH 162
Cdd:PRK06310 80 QIKGFFKEGDYIVgHSVGFDLQVLSQESERIGETfLSKHYYI---IDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--H 154
|
170
....*....|...
gi 16128202 163 GALLDAQILAEVY 175
Cdd:PRK06310 155 RAMKDVEINIKVF 167
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
3-175 |
1.87e-10 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 59.27 E-value: 1.87e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 3 TAITRQI--VLDTETTGMNQigahyEGHKIIEIGAVEVVNRRLTgNNFHVYLKPDRLvdPEAFG-VHGIADEFLLDKPTF 79
Cdd:PRK08517 63 TPIKDQVfcFVDIETNGSKP-----KKHQIIEIGAVKVKNGEII-DRFESFVKAKEV--PEYITeLTGITYEDLENAPSL 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 80 AEVADEFMDYIRGAELVIHNAAFDIGFMDYEFS------LLKRDIpktntfckvtDSLAVARKMFPGKRNSLDALCARYE 153
Cdd:PRK08517 135 KEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEeiglgpLLNRKL----------CTIDLAKRTIESPRYGLSFLKELLG 204
|
170 180
....*....|....*....|..
gi 16128202 154 IDNSkrTLHGALLDAQILAEVY 175
Cdd:PRK08517 205 IEIE--VHHRAYADALAAYEIF 224
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
9-178 |
6.10e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 51.90 E-value: 6.10e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTgnnfhvylkpdRLVDP------EAFGVHGIADEFLLDK-----P 77
Cdd:PRK07942 9 AAFDLETTGVDPETARIVTAALVVVDADGEVVESRE-----------WLADPgveipeEASAVHGITTEYARAHgrpaaE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 78 TFAEVADEFMDYIR-GAELVIHNAAFDIGFMDYEfsLLKRDIPKTNTFcKVTDSLAVARKMFP---GKRNsLDALCARYE 153
Cdd:PRK07942 78 VLAEIADALREAWArGVPVVVFNAPYDLTVLDRE--LRRHGLPSLVPG-PVIDPYVIDKAVDRyrkGKRT-LTALCEHYG 153
|
170 180
....*....|....*....|....*..
gi 16128202 154 I--DNSkrtlHGALLDAQILAEVYLAM 178
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 ... |
7-91 |
1.95e-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: 1.95e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTETTGMNQIGAhyeghKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVdPEAFGVHGIADEFLLDKP-TFAEVADE 85
Cdd:pfam13361 187 NIVVFDVETTGLDTTED-----EIIQIAAIKLNKKGVVIESFERFLRLKKPV-GDSLQVHGFSDEFLQENGeTPAEALRD 260
|
....*.
gi 16128202 86 FMDYIR 91
Cdd:pfam13361 261 FLEKLE 266
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
9-108 |
2.35e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 50.36 E-value: 2.35e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQigahyEGHKIIEIGAV-----------EVVNRrltgnnFHVYLKPDRLVDPEAFGVHGIADEFLLDKP 77
Cdd:PRK09182 40 VILDTETTGLDP-----RKDEIIEIGMVafeydddgrigDVLDT------FGGLQQPSRPIPPEITRLTGITDEMVAGQT 108
|
90 100 110
....*....|....*....|....*....|..
gi 16128202 78 TFAEVADEFMDyirGAELVI-HNAAFDIGFMD 108
Cdd:PRK09182 109 IDPAAVDALIA---PADLIIaHNAGFDRPFLE 137
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
33-143 |
3.23e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 50.16 E-value: 3.23e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 33 IGAVEVVNRRLTGNNFHVyLKPDRLV-DPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEF 111
Cdd:PRK06195 21 IGIVVVKDGEIVEKVHYL-IKPKEMRfMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTL 99
|
90 100 110
....*....|....*....|....*....|..
gi 16128202 112 SLLKRDIPKTNTFCkvtdSLAVARKMFPGKRN 143
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 ... |
9-178 |
5.52e-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: 48.37 E-value: 5.52e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 9 IVLDTETTGMNQIGAHYEGHKIIEIGAVEV-VNRRLTGNNFHVYLKPdrLVDPEAF----GVHGIADEFLLDKPTFAEVA 83
Cdd:cd06133 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVdVKTKEIIDTFSSYVKP--VINPKLSdfctELTGITQEDVDNAPSFPEVL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 84 DEFMDYIRGAElvihNAAF------DIGFMDYEFSLLKRdIPKTNTFCKVTD-SLAVARKMFPGKRNSLDALCARYEIDN 156
Cdd:cd06133 80 KEFLEWLGKNG----KYAFvtwgdwDLKDLLQNQCKYKI-INLPPFFRQWIDlKKEFAKFYGLKKRTGLSKALEYLGLEF 154
|
170 180
....*....|....*....|..
gi 16128202 157 SKRTlHGALLDAQILAEVYLAM 178
Cdd:cd06133 155 EGRH-HRGLDDARNIARILKRL 175
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
11-108 |
2.94e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 46.84 E-value: 2.94e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 11 LDTETTGMNQigahyEGHKIIEIGAVEV-VNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDY 89
Cdd:PRK09146 52 LDFETTGLDA-----EQDAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEA 126
|
90
....*....|....*....
gi 16128202 90 IRGAELVIHNAAFDIGFMD 108
Cdd:PRK09146 127 LAGKVVVVHYRRIERDFLD 145
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
22-122 |
5.05e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 43.66 E-value: 5.05e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 22 GAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRlvDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAA 101
Cdd:PRK05601 57 GIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGE--DPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAP 134
|
90 100
....*....|....*....|.
gi 16128202 102 FDIGFMDYEFSLLKRDIPKTN 122
Cdd:PRK05601 135 RTWGFIVSEAKRAMNAAARAN 155
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
7-180 |
6.06e-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: 6.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 7 RQIVLDTEttgMNQI-GAHYEGHK--IIEIGAVEV-VNRRLTGnNFHVYLKPDR--LVDPEAFGVHGIADEFLLDKPTFA 80
Cdd:COG5018 3 KYLVIDLE---ATCWdGKPPPGFPmeIIEIGAVKVdENGEIID-EFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 81 EVADEFMDYIRGAELVIhnaafdIGFMDYEFSLLKRDIpktnTFCKVTDSL-----------AVARKMfpGKRNSLDALC 149
Cdd:COG5018 79 EAIEDFKKWIGSEDYIL------CSWGDYDRKQLERNC----RFHGVPYPFgdrhinlkklfALYFGL--KKRIGLKKAL 146
|
170 180 190
....*....|....*....|....*....|.
gi 16128202 150 ARYEIDNsKRTLHGALLDAQILAEVYLAMTG 180
Cdd:COG5018 147 ELLGLEF-EGTHHRALDDARNTAKLFKKILG 176
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-176 |
5.72e-04 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 40.83 E-value: 5.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 1 MSTAITRQ-IVLDTETTGmnqigAHYEGhKIIEIGAVEVVNRRLTgNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTF 79
Cdd:PRK07246 1 MTQKKLRKyAVVDLEATG-----AGPNA-SIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDF 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128202 80 AEVADEFMDYIRGAELVIHNAAFDIG------FMD-YEFSllkrdIPKtntfckvTDSLAVARKMFPG-KRNSLDALCAR 151
Cdd:PRK07246 74 SQVARHIYDLIEDCIFVAHNVKFDANllaealFLEgYELR-----TPR-------VDTVELAQVFFPTlEKYSLSHLSRE 141
|
170 180
....*....|....*....|....*
gi 16128202 152 YEIDNSKRtlHGALLDAQILAEVYL 176
Cdd:PRK07246 142 LNIDLADA--HTAIADARATAELFL 164
|
|
| |
