|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-233 |
3.19e-142 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 397.69 E-value: 3.19e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 1 MRQIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 81 IDGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQ 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAE 163
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1535725758 161 ILGDVYIALTSGQEEIGFGLGDEDGGGAGAALQAFDTSKLLPRPRVVATPSELEAHAARLERLRKKAGHALWD 233
Cdd:PRK05711 164 ILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-227 |
3.55e-114 |
|
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: 326.27 E-value: 3.55e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQI 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1535725758 162 LGDVYIALTSGQEEIGFGLGDEDGGGAGAALQAFDtSKLLPRPRVVATPSELEAHAARLERLRKKA 227
Cdd:TIGR01406 161 LAEVYLALTGGQESLLELAESNSGEAAKPSKSAEM-KLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
3-170 |
1.13e-98 |
|
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: 284.81 E-value: 1.13e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 3 QIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFID 82
Cdd:cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 83 GAELIIHNAAFDLGFLDNELSLLGPQyGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQIL 162
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLG-KKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELL 159
|
....*...
gi 1535725758 163 GDVYIALT 170
Cdd:cd06131 160 AEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
2-170 |
5.93e-63 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 193.86 E-value: 5.93e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVELFKRRPTgNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:COG0847 1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYgkitDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRalHGGLLDAQ 160
Cdd:COG0847 79 GGAVLVAHNAAFDLGFLNAELRRAGLPL----PPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAE 152
|
170
....*....|
gi 1535725758 161 ILGDVYIALT 170
Cdd:COG0847 153 ATAELFLALL 162
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
2-170 |
1.49e-41 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 139.74 E-value: 1.49e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVELFKRRpTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:smart00479 1 TLVVIDCETTGLDPGK-DEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHN-AAFDLGFLDNELSLLGPqygKITDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRAlHGGLLDA 159
Cdd:smart00479 79 RGRILVAGNsAHFDLRFLKLEHPRLGI---KQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRALDDA 154
|
170
....*....|.
gi 1535725758 160 QILGDVYIALT 170
Cdd:smart00479 155 RATAKLFKKLL 165
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-166 |
8.07e-31 |
|
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: 111.67 E-value: 8.07e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEwKKGNRIVEIGCVEL-FKRRPTGNNYHQYIKPDC--EFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAF 80
Cdd:pfam00929 1 VVIDLETTGLD-PEKDEIIEIAAVVIdGGENEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 81 ID-GAELIIHNAAFDLGFLDNELSLLGPQYgkITDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRAlHGGLLD 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLKKP--MPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGRA-HRALDD 156
|
....*...
gi 1535725758 159 AQILGDVY 166
Cdd:pfam00929 157 ARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-233 |
3.19e-142 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 397.69 E-value: 3.19e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 1 MRQIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 81 IDGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQ 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAE 163
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1535725758 161 ILGDVYIALTSGQEEIGFGLGDEDGGGAGAALQAFDTSKLLPRPRVVATPSELEAHAARLERLRKKAGHALWD 233
Cdd:PRK05711 164 ILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCLWR 236
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-227 |
3.55e-114 |
|
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: 326.27 E-value: 3.55e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQI 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1535725758 162 LGDVYIALTSGQEEIGFGLGDEDGGGAGAALQAFDtSKLLPRPRVVATPSELEAHAARLERLRKKA 227
Cdd:TIGR01406 161 LAEVYLALTGGQESLLELAESNSGEAAKPSKSAEM-KLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
3-170 |
1.13e-98 |
|
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: 284.81 E-value: 1.13e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 3 QIILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFID 82
Cdd:cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 83 GAELIIHNAAFDLGFLDNELSLLGPQyGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLLDAQIL 162
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLG-KKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELL 159
|
....*...
gi 1535725758 163 GDVYIALT 170
Cdd:cd06131 160 AEVYLELT 167
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
2-170 |
5.93e-63 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 193.86 E-value: 5.93e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVELFKRRPTgNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:COG0847 1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYgkitDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRalHGGLLDAQ 160
Cdd:COG0847 79 GGAVLVAHNAAFDLGFLNAELRRAGLPL----PPFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAE 152
|
170
....*....|
gi 1535725758 161 ILGDVYIALT 170
Cdd:COG0847 153 ATAELFLALL 162
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
2-176 |
6.64e-61 |
|
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: 190.74 E-value: 6.64e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLE----WKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEF 77
Cdd:TIGR00573 2 RQLVLDTETTGDNettgLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 78 LAFIDGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGVDNSHRALHGGLL 157
Cdd:TIGR00573 82 ADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALA 161
|
170
....*....|....*....
gi 1535725758 158 DAQILGDVYIALTSGQEEI 176
Cdd:TIGR00573 162 DAFILAKLYLVMTGKQTKY 180
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
4-167 |
1.85e-43 |
|
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: 143.98 E-value: 1.85e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEwKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDG 83
Cdd:cd06127 1 VVFDTETTGLD-PKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 84 AELIIHNAAFDLGFLDNELsllgPQYGKITDRCTVIDTLVMARERFPGQRNSL--DALCKRLGVD--NSHRALHggllDA 159
Cdd:cd06127 80 RVLVAHNASFDLRFLNREL----RRLGGPPLPNPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPleGAHRALA----DA 151
|
....*...
gi 1535725758 160 QILGDVYI 167
Cdd:cd06127 152 LATAELLL 159
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
4-169 |
3.17e-43 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 144.13 E-value: 3.17e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKgNRIVEIGCVELFKRRPTGNnYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDG 83
Cdd:COG2176 11 VVFDLETTGLSPKK-DEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 84 AELIIHNAAFDLGFLDNELSLLGPQYgkitdRCTVIDTLVMARERFPGQRN-SLDALCKRLGV--DNSHRALHggllDAQ 160
Cdd:COG2176 89 AVLVAHNASFDLGFLNAALKRLGLPF-----DNPVLDTLELARRLLPELKSyKLDTLAERLGIplEDRHRALG----DAE 159
|
....*....
gi 1535725758 161 ILGDVYIAL 169
Cdd:COG2176 160 ATAELFLKL 168
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
2-170 |
1.49e-41 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 139.74 E-value: 1.49e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVELFKRRpTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:smart00479 1 TLVVIDCETTGLDPGK-DEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHN-AAFDLGFLDNELSLLGPqygKITDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRAlHGGLLDA 159
Cdd:smart00479 79 RGRILVAGNsAHFDLRFLKLEHPRLGI---KQPPKLPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQRA-HRALDDA 154
|
170
....*....|.
gi 1535725758 160 QILGDVYIALT 170
Cdd:smart00479 155 RATAKLFKKLL 165
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-166 |
8.07e-31 |
|
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: 111.67 E-value: 8.07e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEwKKGNRIVEIGCVEL-FKRRPTGNNYHQYIKPDC--EFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAF 80
Cdd:pfam00929 1 VVIDLETTGLD-PEKDEIIEIAAVVIdGGENEIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 81 ID-GAELIIHNAAFDLGFLDNELSLLGPQYgkITDRCTVIDTLVMARERFPG-QRNSLDALCKRLGVDNSHRAlHGGLLD 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLKKP--MPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGRA-HRALDD 156
|
....*...
gi 1535725758 159 AQILGDVY 166
Cdd:pfam00929 157 ARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
5-167 |
4.16e-27 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 109.16 E-value: 4.16e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 5 ILDTETTGLEWKKgNRIVEIGCVELFKrrptGN---NYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:PRK00448 423 VFDVETTGLSAVY-DEIIEIGAVKIKN----GEiidKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFC 497
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGpqYGKITdrCTVIDTLVMARERFPGQRN-SLDALCKRLGV--DNSHRALHggllD 158
Cdd:PRK00448 498 GDSILVAHNASFDVGFINTNYEKLG--LEKIK--NPVIDTLELSRFLYPELKShRLNTLAKKFGVelEHHHRADY----D 569
|
....*....
gi 1535725758 159 AQILGDVYI 167
Cdd:PRK00448 570 AEATAYLLI 578
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-169 |
1.91e-26 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 107.35 E-value: 1.91e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 1 MRQIILDTETTGLEWKKGNRIVEIGCV-----ELFKRrptgnnYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIAD 75
Cdd:PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVvvedgEILER------FSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 76 EFLAFIDGAELIIHNAAFDLGFLDNELSLLGpqYGKITdrCTVIDTLVMARERFPGQRN-SLDALCKRLGV--DNSHRAL 152
Cdd:PRK08074 77 EIVELLEGAYFVAHNVHFDLNFLNEELERAG--YTEIH--CPKLDTVELARILLPTAESyKLRDLSEELGLehDQPHRAD 152
|
170
....*....|....*..
gi 1535725758 153 HggllDAQILGDVYIAL 169
Cdd:PRK08074 153 S----DAEVTAELFLQL 165
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
4-169 |
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 1535725758 4 IILDTETTGLEWKKGNRIVEIGCVELFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDG 83
Cdd:PRK07740 62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGA 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 84 AELIIHNAAFDLGFLDNELSllgpQYGKITDRCTVIDTLVMARERFPGQRN-SLDALCKRLGVD--NSHRALHGGLLDAQ 160
Cdd:PRK07740 142 GVLVAHHAGHDKAFLRHALW----RTYRQPFTHRLIDTMFLTKLLAHERDFpTLDDALAYYGIPipRRHHALGDALMTAK 217
|
170 180
....*....|....*....|....
gi 1535725758 161 I---------------LGDVYIAL 169
Cdd:PRK07740 218 LwaillveaqqrgittLHDLYAAL 241
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
12-162 |
2.69e-18 |
|
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.
Pssm-ID: 99834 [Multi-domain] Cd Length: 156 Bit Score: 78.71 E-value: 2.69e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 12 GLEWKKGNRIVEigcvelfkrrptgnNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDGAELIIHNA 91
Cdd:cd06130 20 GLVKVRDGQIVD--------------TFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNA 85
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1535725758 92 AFDLGFLDNELSLlgpqYGKITDRCTVIDTLVMARERFPGQRN-SLDALCKRLGVD-NSHRALHGGLLDAQIL 162
Cdd:cd06130 86 SFDRSVLRAALEA----YGLPPPPYQYLCTVRLARRVWPLLPNhKLNTVAEHLGIElNHHDALEDARACAEIL 154
|
|
| dinG_rel |
TIGR01407 |
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ... |
2-169 |
3.92e-17 |
|
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273602 [Multi-domain] Cd Length: 850 Bit Score: 80.23 E-value: 3.92e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVeLFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:TIGR01407 1 RYAVVDLETTGTQLSF-DKIIQIGIV-VVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYGKItdrcTVIDTLVMARERFPGQRN-SLDALCKRLGV--DNSHRALHggllD 158
Cdd:TIGR01407 79 EDGIFVAHNVHFDLNFLAKALKDCGYEPLPK----PRIDTVELAQIFFPTEESyQLSELSEALGLthENPHRADS----D 150
|
170
....*....|.
gi 1535725758 159 AQILGDVYIAL 169
Cdd:TIGR01407 151 AQATAELLLLL 161
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
4-175 |
6.07e-17 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 78.32 E-value: 6.07e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEwKKGNRIVEIGCVElFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDG 83
Cdd:PRK06807 11 VVIDFETTGFN-PYNDKIIQVAAVK-YRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 84 AELIIHNAAFDLGFLDNELSLLGPQYGKitdrCTVIDTLVMARERFPGQRN-SLDALCKRLGVD-NSHRALHggllDAQI 161
Cdd:PRK06807 89 NVIVAHNASFDMRFLKSNVNMLGLPEPK----NKVIDTVFLAKKYMKHAPNhKLETLKRMLGIRlSSHNAFD----DCIT 160
|
170
....*....|....
gi 1535725758 162 LGDVYIALTSGQEE 175
Cdd:PRK06807 161 CAAVYQKCASIEEE 174
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
4-152 |
2.58e-15 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 72.94 E-value: 2.58e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKgNRIVEIGCVElFKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDG 83
Cdd:PRK06310 10 VCLDCETTGLDVKK-DRIIEFAAIR-FTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKE 87
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1535725758 84 AELII-HNAAFDLGFLDNELSLLGPQygKITDRCTVIDTLVMARERFPGQRNSLDALCKRLGV--DNSHRAL 152
Cdd:PRK06310 88 GDYIVgHSVGFDLQVLSQESERIGET--FLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVpyDGNHRAM 157
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
5-162 |
2.04e-12 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 64.66 E-value: 2.04e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 5 ILDTETTGlEWKKGNRIVEIGCVElFKRRPTGNNYHQYIKPDcEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDGA 84
Cdd:PRK08517 72 FVDIETNG-SKPKKHQIIEIGAVK-VKNGEIIDRFESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGDS 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 85 ELIIHNAAFDLGFLDNELSLLGpqYGKITDR--CTvIDtlvMARERFPGQRNSLDALCKRLGVDN--SHRALHGGLLDAQ 160
Cdd:PRK08517 149 VFVAHNVNFDYNFISRSLEEIG--LGPLLNRklCT-ID---LAKRTIESPRYGLSFLKELLGIEIevHHRAYADALAAYE 222
|
..
gi 1535725758 161 IL 162
Cdd:PRK08517 223 IF 224
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
7-169 |
4.28e-12 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 64.94 E-value: 4.28e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 7 DTETTGLEwKKGNRIVEIGCV-----ELFKRRPTGNNYHQYIKPDcefeqgAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:PRK07883 21 DLETTGGS-PAGDAITEIGAVkvrggEVLGEFATLVNPGRPIPPF------ITVLTGITTAMVAGAPPIEEVLPAFLEFA 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLG---PQYgkitdrcTVIDTLVMARERFPGQ---RNSLDALCKRLGVD--NSHRALH 153
Cdd:PRK07883 94 RGAVLVAHNAPFDIGFLRAAAARCGypwPGP-------PVLCTVRLARRVLPRDeapNVRLSTLARLFGATttPTHRALD 166
|
170
....*....|....*.
gi 1535725758 154 ggllDAQILGDVYIAL 169
Cdd:PRK07883 167 ----DARATVDVLHGL 178
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
5-165 |
1.35e-11 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 63.18 E-value: 1.35e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 5 ILDTETTGLEwKKGNRIVEIGCVELfkrRPTGNNYHQY---IKPDCEfeQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:PRK06063 19 VVDVETSGFR-PGQARIISLAVLGL---DADGNVEQSVvtlLNPGVD--PGPTHVHGLTAEMLEGQPQFADIAGEVAELL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCTVidtlVMARE-RFPGQRNSLDALCKRLGVDNsHRAlHGGLLDAQ 160
Cdd:PRK06063 93 RGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTV----ELARRlGLGLPNLRLETLAAHWGVPQ-QRP-HDALDDAR 166
|
....*
gi 1535725758 161 ILGDV 165
Cdd:PRK06063 167 VLAGI 171
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
2-169 |
2.75e-09 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 55.59 E-value: 2.75e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 2 RQIILDTETTGLEWKKgNRIVEIGCVElfkrRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFI 81
Cdd:PRK06309 3 ALIFYDTETTGTQIDK-DRIIEIAAYN----GVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 82 DG-AELIIHNA-AFDLGFLDNEL---SLLGPQYgkitdrcTVIDTLVMARERFPG-QRNSLDALCKRLGV--DNSHRALH 153
Cdd:PRK06309 78 GTdNILVAHNNdAFDFPLLRKECrrhGLEPPTL-------RTIDSLKWAQKYRPDlPKHNLQYLRQVYGFeeNQAHRALD 150
|
170
....*....|....*.
gi 1535725758 154 ggllDAQILGDVYIAL 169
Cdd:PRK06309 151 ----DVITLHRVFSAL 162
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
4-99 |
6.51e-09 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 54.98 E-value: 6.51e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKgNRIVEIGCVeLFKRRPTGN------NYHQYIKPDCEFEQGAQEVTGLTLEFLDDKP-DFAQIAde 76
Cdd:PRK09182 40 VILDTETTGLDPRK-DEIIEIGMV-AFEYDDDGRigdvldTFGGLQQPSRPIPPEITRLTGITDEMVAGQTiDPAAVD-- 115
|
90 100
....*....|....*....|....
gi 1535725758 77 flAFIDGAELII-HNAAFDLGFLD 99
Cdd:PRK09182 116 --ALIAPADLIIaHNAGFDRPFLE 137
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
7-151 |
2.39e-08 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 53.06 E-value: 2.39e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 7 DTETTGLEwKKGNRIVEiGCVELFKRRPTGNNYHQYI-KPDCEFEQGAQEVTGLTLEFL-----DDKPDFAQIADEFLA- 79
Cdd:PRK07942 12 DLETTGVD-PETARIVT-AALVVVDADGEVVESREWLaDPGVEIPEEASAVHGITTEYArahgrPAAEVLAEIADALREa 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1535725758 80 FIDGAELIIHNAAFDLGFLDNELsllgPQYGKIT-DRCTVIDTLVMARE--RF-PGQRNsLDALCKRLGV--DNSHRA 151
Cdd:PRK07942 90 WARGVPVVVFNAPYDLTVLDREL----RRHGLPSlVPGPVIDPYVIDKAvdRYrKGKRT-LTALCEHYGVrlDNAHEA 162
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
55-169 |
2.93e-07 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 50.84 E-value: 2.93e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 55 EVTGLTLEFLDDKPDFAQIADEFLAFIDGAELIIHNAAFDLGFLDNELSLLGpqYGKITDRctvIDTLVMARERFPG-QR 133
Cdd:PRK07246 58 HLTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALFLEG--YELRTPR---VDTVELAQVFFPTlEK 132
|
90 100 110
....*....|....*....|....*....|....*.
gi 1535725758 134 NSLDALCKRLGVDNSHRalHGGLLDAQILGDVYIAL 169
Cdd:PRK07246 133 YSLSHLSRELNIDLADA--HTAIADARATAELFLKL 166
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
5-172 |
3.37e-07 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 49.33 E-value: 3.37e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 5 ILDTETTGLEwkkgNRIVEIGCVELFKRRPTgNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLafidGA 84
Cdd:PRK07983 4 VIDTETCGLQ----GGIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY----GS 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 85 EL-IIHNAAFDLGFLdnelsllgPQYGKitdrcTVIDTLVMARERFPGQRNSLDALCKRLGVD-------NSHRALHGGL 156
Cdd:PRK07983 75 EWyVAHNASFDRRVL--------PEMPG-----EWICTMKLARRLWPGIKYSNMALYKSRKLNvqtppglHHHRALYDCY 141
|
170
....*....|....*.
gi 1535725758 157 LDAQILgdVYIALTSG 172
Cdd:PRK07983 142 ITAALL--IDIMNTSG 155
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
40-159 |
6.29e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 49.39 E-value: 6.29e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 40 HQYIKPdCE--FEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDGAELIIHNAAFDLGFLDNELSLLGPQYGKITDRCT 117
Cdd:PRK06195 36 HYLIKP-KEmrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICT 114
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1535725758 118 VidtlVMARERFPGQRNS-LDALCKRLGVDNSHralHGGLLDA 159
Cdd:PRK06195 115 M----KLAKNFYSNIDNArLNTVNNFLGYEFKH---HDALADA 150
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
6-143 |
9.80e-07 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 48.38 E-value: 9.80e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 6 LDTETTGLEWKKgNRIVEIGCVEL-FKRRPTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDGA 84
Cdd:PRK09146 52 LDFETTGLDAEQ-DAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGK 130
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1535725758 85 ELIIHNAAFDLGFLDNEL-SLLG-----PqygkitdrctVIDTLVMARERfpgQRNSLDALCKRL 143
Cdd:PRK09146 131 VVVVHYRRIERDFLDQALrNRIGegiefP----------VIDTMEIEARI---QRKQAGGLWNRL 182
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
4-174 |
1.40e-06 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 47.59 E-value: 1.40e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKgNRIVEIGCVELFKRR-PTGNNYHQYIKPDCEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFID 82
Cdd:PRK09145 32 VALDCETTGLDPRR-AEIVSIAAVKIRGNRiLTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIG 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 83 GAELIIHNAAFDLGFLDnelSLLGPQYGkITDRCTVIDTLVM----ARERFPG--QRNSLDALCKRLGVDNSHRalHGGL 156
Cdd:PRK09145 111 NRPLVGYYLEFDVAMLN---RYVRPLLG-IPLPNPLIEVSALyydkKERHLPDayIDLRFDAILKHLDLPVLGR--HDAL 184
|
170
....*....|....*...
gi 1535725758 157 LDAQILGDVYIALTSGQE 174
Cdd:PRK09145 185 NDAIMAALIFLRLRKGDA 202
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
20-101 |
9.82e-05 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 42.89 E-value: 9.82e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 20 RIVEIGCVELFKRRPTGNNYHQYIKPdcEFEQGAQEVTGLTLEFLDDKPDFAQIADEFLAFIDGAELIIHNAAFDLGFLD 99
Cdd:PRK05601 64 RLITIDAVTLTADGEEVEHFHAVLNP--GEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIV 141
|
..
gi 1535725758 100 NE 101
Cdd:PRK05601 142 SE 143
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
4-151 |
6.15e-04 |
|
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.
Pssm-ID: 99839 [Multi-domain] Cd Length: 177 Bit Score: 39.62 E-value: 6.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKGNRIVEIgCVELFKRRPTGNNYHQY-------------IKPDCEFEQGAQEVTGLTLEFLDDKPDF 70
Cdd:cd06136 2 VFLDLETTGLPKHNRPEITEL-CLVAVHRDHLLNTSRDKpalprvldklslcFNPGRAISPGASEITGLSNDLLEHKAPF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 71 -AQIADEFLAFIDGAE----LIIHNA-AFDLGFLDNELSLLGpqyGKITDRCTVIDTLVMARERFpgqrNSLDALCKRL- 143
Cdd:cd06136 81 dSDTANLIKLFLRRQPkpicLVAHNGnRFDFPILRSELERLG---TKLPDDILCVDSLPAFRELD----QSLGSLYKRLf 153
|
170
....*....|
gi 1535725758 144 GVD--NSHRA 151
Cdd:cd06136 154 GQEpkNSHTA 163
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
4-146 |
6.53e-04 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 39.12 E-value: 6.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKGNrIVEIGCveLFKRRPTGNNYHQYIKPDCEFEqgaqevtgltleflddkpdfAQIADEFLAFIDG 83
Cdd:pfam13482 1 LFFDIETTGLSPGKNT-IYLIGV--YDVDGDKVRTFVQYLAEGPTEE--------------------AAILQLFELLADY 57
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1535725758 84 AELIIHN-AAFDLGFLDNELSLLGPQYGKITdrctvIDtlVMARERFPGQRNSLDALCKRLGVD 146
Cdd:pfam13482 58 PLLVTFNgKSFDVPFIKRRFKRYDLDELFRH-----ID--LLHPLRKLGLESGLKSVERELGIE 114
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
4-81 |
1.05e-03 |
|
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: 38.74 E-value: 1.05e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEWKKG----NRIVEIGCVEL-FKRRPTGNNYHQYIKPD--------CEfeqgaqEVTGLTLEFLDDKPDF 70
Cdd:cd06133 2 LVIDFEATCWEGNSKpdypNEIIEIGAVLVdVKTKEIIDTFSSYVKPVinpklsdfCT------ELTGITQEDVDNAPSF 75
|
90
....*....|.
gi 1535725758 71 AQIADEFLAFI 81
Cdd:cd06133 76 PEVLKEFLEWL 86
|
|
| YprB |
COG3359 |
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ... |
4-109 |
6.63e-03 |
|
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];
Pssm-ID: 442587 [Multi-domain] Cd Length: 198 Bit Score: 36.46 E-value: 6.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1535725758 4 IILDTETTGLEwKKGNRIVEIGcveLFKRRPTGNNYHQYikpdcefeqgaqevtgltleFLDDKPDFAQIADEFLAFIDG 83
Cdd:COG3359 18 LFFDIETTGLS-GGGTVIFLIG---LADGEGDGFVVRQY--------------------FGEDPGEEAALLEAFLEWLAD 73
|
90 100
....*....|....*....|....*...
gi 1535725758 84 AELIIH-N-AAFDLGFLDNELSLLGPQY 109
Cdd:COG3359 74 YKLLVTyNgKSFDLPFLKTRFTLHRLPP 101
|
|
| |
