|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-240 |
3.89e-142 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 397.31 E-value: 3.89e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 1 MRQIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 81 CDGAELVIHNAPFDVGFIDSELKRLGSPRwQNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDA 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDI-PKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 161 EILADVYLIMTGGQTDL-LASNDASGEADQKQEasaaepgaIRRLSAERASLNVVRANEQELDAHAAFLALLEKSGGKHF 239
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLgFAMEGETQQQQGEET--------IQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCL 234
|
.
gi 2087741084 240 W 240
Cdd:PRK05711 235 W 235
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
3-171 |
2.17e-111 |
|
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: 316.78 E-value: 2.17e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 3 QIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCD 82
Cdd:cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 83 GAELVIHNAPFDVGFIDSELKRLGSPRwqNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDAEI 162
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLGK--KIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAEL 158
|
....*....
gi 2087741084 163 LADVYLIMT 171
Cdd:cd06131 159 LAEVYLELT 167
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-235 |
1.93e-110 |
|
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: 316.64 E-value: 1.93e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHNAPFDVGFIDSELKRLGsPRWQNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDAE 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLG-PTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2087741084 162 ILADVYLIMTGGQTDLLAS-NDASGEADQKqeasaaepgAIRRLSAERASLNVVRANEQELDAHAAFLALLEKSG 235
Cdd:TIGR01406 160 LLAEVYLALTGGQESLLELaESNSGEAAKP---------SKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
2-172 |
1.04e-69 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 211.19 E-value: 1.04e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKSgHRIIEIGCVELINRKLTgRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:COG0847 1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHNAPFDVGFIDSELKRLGSPRWqnvatHCGVLDTLALAREKHPG-QKNNLDALCKRYFVDNSQRdlHGALLDA 160
Cdd:COG0847 79 GGAVLVAHNAAFDLGFLNAELRRAGLPLP-----PFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADA 151
|
170
....*....|..
gi 2087741084 161 EILADVYLIMTG 172
Cdd:COG0847 152 EATAELFLALLR 163
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
2-172 |
1.32e-49 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 160.16 E-value: 1.32e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKsGHRIIEIGCVELINRKlTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:smart00479 1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHN-APFDVGFIDSELKRLGSPRWQNvathCGVLDTLALAREKHPG-QKNNLDALCKRYFVDNSQRdLHGALLD 159
Cdd:smart00479 79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPK----LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDD 153
|
170
....*....|...
gi 2087741084 160 AEILADVYLIMTG 172
Cdd:smart00479 154 ARATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-167 |
1.84e-41 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 139.02 E-value: 1.84e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKsGHRIIEIGCVELINRKL-TGRHYHQYINPER--EVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTF 80
Cdd:pfam00929 1 VVIDLETTGLDPE-KDEIIEIAAVVIDGGENeIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 81 CD-GAELVIHNAPFDVGFIDSELKRLGSprwQNVATHCGVLDTLALAREKHPGQKNN-LDALCKRYFVDNSQRdLHGALL 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLK---KPMPKLNPVIDTLILDKATYKELPGRsLDALAEKLGLEHIGR-AHRALD 155
|
....*....
gi 2087741084 159 DAEILADVY 167
Cdd:pfam00929 156 DARATAKLF 164
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
1-240 |
3.89e-142 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 397.31 E-value: 3.89e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 1 MRQIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTF 80
Cdd:PRK05711 4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 81 CDGAELVIHNAPFDVGFIDSELKRLGSPRwQNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDA 160
Cdd:PRK05711 84 IRGAELIIHNAPFDIGFMDYEFALLGRDI-PKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 161 EILADVYLIMTGGQTDL-LASNDASGEADQKQEasaaepgaIRRLSAERASLNVVRANEQELDAHAAFLALLEKSGGKHF 239
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLgFAMEGETQQQQGEET--------IQRIVRQRSRLPVVRATDEELAAHEARLDLLDKKGGSCL 234
|
.
gi 2087741084 240 W 240
Cdd:PRK05711 235 W 235
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
3-171 |
2.17e-111 |
|
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: 316.78 E-value: 2.17e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 3 QIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCD 82
Cdd:cd06131 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 83 GAELVIHNAPFDVGFIDSELKRLGSPRwqNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDAEI 162
Cdd:cd06131 81 GAELVIHNASFDVGFLNAELSLLGLGK--KIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAEL 158
|
....*....
gi 2087741084 163 LADVYLIMT 171
Cdd:cd06131 159 LAEVYLELT 167
|
|
| dnaQ_proteo |
TIGR01406 |
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ... |
2-235 |
1.93e-110 |
|
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: 316.64 E-value: 1.93e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:TIGR01406 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHNAPFDVGFIDSELKRLGsPRWQNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGALLDAE 161
Cdd:TIGR01406 81 GGSELVIHNAAFDVGFLNYELERLG-PTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2087741084 162 ILADVYLIMTGGQTDLLAS-NDASGEADQKqeasaaepgAIRRLSAERASLNVVRANEQELDAHAAFLALLEKSG 235
Cdd:TIGR01406 160 LLAEVYLALTGGQESLLELaESNSGEAAKP---------SKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
2-172 |
1.04e-69 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 211.19 E-value: 1.04e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKSgHRIIEIGCVELINRKLTgRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:COG0847 1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHNAPFDVGFIDSELKRLGSPRWqnvatHCGVLDTLALAREKHPG-QKNNLDALCKRYFVDNSQRdlHGALLDA 160
Cdd:COG0847 79 GGAVLVAHNAAFDLGFLNAELRRAGLPLP-----PFPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADA 151
|
170
....*....|..
gi 2087741084 161 EILADVYLIMTG 172
Cdd:COG0847 152 EATAELFLALLR 163
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
2-224 |
2.30e-64 |
|
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: 199.60 E-value: 2.30e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLD----PKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEF 77
Cdd:TIGR00573 2 RQLVLDTETTGDNettgLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 78 MTFCDGAELVIHNAPFDVGFIDSELKRLgSPRWQNVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRDLHGAL 157
Cdd:TIGR00573 82 ADYIRGAELVIHNASFDVGFLNYEFSKL-YKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2087741084 158 LDAEILADVYLIMTGGQTDLlasndasGEADQKQEASAAEPGAIRRLSaerASLNVVRANEQELDAH 224
Cdd:TIGR00573 161 ADAFILAKLYLVMTGKQTKY-------GENEGQQSRPYHAIKSIVKKD---MLLKLIKAVSTELQAH 217
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
4-170 |
7.02e-54 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 171.48 E-value: 7.02e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVELINRKLTGRhYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:COG2176 11 VVFDLETTGLSPKK-DEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 84 AELVIHNAPFDVGFIDSELKRLGSPrWQNVathcgVLDTLALAREKHPGQKN-NLDALCKRYFVDNSQRdlHGALLDAEI 162
Cdd:COG2176 89 AVLVAHNASFDLGFLNAALKRLGLP-FDNP-----VLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGDAEA 160
|
....*...
gi 2087741084 163 LADVYLIM 170
Cdd:COG2176 161 TAELFLKL 168
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
4-168 |
1.95e-50 |
|
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: 161.70 E-value: 1.95e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKsGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:cd06127 1 VVFDTETTGLDPK-KDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 84 AELVIHNAPFDVGFIDSELKRLGSPRWQNVathcgVLDTLALAREKHPGQKNNL--DALCKRYFVDNSQRdlHGALLDAE 161
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNP-----WIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALADAL 152
|
....*..
gi 2087741084 162 ILADVYL 168
Cdd:cd06127 153 ATAELLL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
2-172 |
1.32e-49 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 160.16 E-value: 1.32e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKsGHRIIEIGCVELINRKlTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:smart00479 1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHN-APFDVGFIDSELKRLGSPRWQNvathCGVLDTLALAREKHPG-QKNNLDALCKRYFVDNSQRdLHGALLD 159
Cdd:smart00479 79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPK----LPVIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDD 153
|
170
....*....|...
gi 2087741084 160 AEILADVYLIMTG 172
Cdd:smart00479 154 ARATAKLFKKLLE 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
4-167 |
1.84e-41 |
|
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;
Pssm-ID: 395743 [Multi-domain] Cd Length: 164 Bit Score: 139.02 E-value: 1.84e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKsGHRIIEIGCVELINRKL-TGRHYHQYINPER--EVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTF 80
Cdd:pfam00929 1 VVIDLETTGLDPE-KDEIIEIAAVVIDGGENeIGETFHTYVKPTRlpKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 81 CD-GAELVIHNAPFDVGFIDSELKRLGSprwQNVATHCGVLDTLALAREKHPGQKNN-LDALCKRYFVDNSQRdLHGALL 158
Cdd:pfam00929 80 LRkGNLLVAHNASFDVGFLRYDDKRFLK---KPMPKLNPVIDTLILDKATYKELPGRsLDALAEKLGLEHIGR-AHRALD 155
|
....*....
gi 2087741084 159 DAEILADVY 167
Cdd:pfam00929 156 DARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
5-170 |
6.89e-36 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 134.58 E-value: 6.89e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLDPKSgHRIIEIGCVELINRKLTGRHyHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK00448 423 VFDVETTGLSAVY-DEIIEIGAVKIKNGEIIDKF-EFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 85 ELVIHNAPFDVGFIDSELKRLGSPRWQNvathcGVLDTLALAREKHPGQKN-NLDALCKRYFVDNSQRdlHGALLDAEIL 163
Cdd:PRK00448 501 ILVAHNASFDVGFINTNYEKLGLEKIKN-----PVIDTLELSRFLYPELKShRLNTLAKKFGVELEHH--HRADYDAEAT 573
|
....*..
gi 2087741084 164 ADVYLIM 170
Cdd:PRK00448 574 AYLLIKF 580
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
1-170 |
1.17e-25 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 105.03 E-value: 1.17e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 1 MRQIVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRhYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTF 80
Cdd:PRK08074 3 KRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEILER-FSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 81 CDGAELVIHNAPFDVGFIDSELKRLGSPRWqnvatHCGVLDTLALAREKHPGQKN-NLDALCKRYFVDNSQRdlHGALLD 159
Cdd:PRK08074 82 LEGAYFVAHNVHFDLNFLNEELERAGYTEI-----HCPKLDTVELARILLPTAESyKLRDLSEELGLEHDQP--HRADSD 154
|
170
....*....|.
gi 2087741084 160 AEILADVYLIM 170
Cdd:PRK08074 155 AEVTAELFLQL 165
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
4-168 |
4.91e-24 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 97.58 E-value: 4.91e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVELINRKLTGRhYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:PRK06807 11 VVIDFETTGFNPYN-DKIIQVAAVKYRNHELVDQ-FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 84 AELVIHNAPFDVGFIDSELKRLGSPRWQNVathcgVLDTLALARE--KH-PGQKnnLDALcKRYFvdNSQRDLHGALLDA 160
Cdd:PRK06807 89 NVIVAHNASFDMRFLKSNVNMLGLPEPKNK-----VIDTVFLAKKymKHaPNHK--LETL-KRML--GIRLSSHNAFDDC 158
|
....*...
gi 2087741084 161 EILADVYL 168
Cdd:PRK06807 159 ITCAAVYQ 166
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
5-166 |
1.18e-23 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 98.84 E-value: 1.18e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLDPKsGHRIIEIGCVELINRKLTGRhYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK07883 19 VVDLETTGGSPA-GDAITEIGAVKVRGGEVLGE-FATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 85 ELVIHNAPFDVGFIDSELKRLGS--PRWQnvathcgVLDTLALAR-----EKHPGQKnnLDALCkRYFvDNSQRDLHGAL 157
Cdd:PRK07883 97 VLVAHNAPFDIGFLRAAAARCGYpwPGPP-------VLCTVRLARrvlprDEAPNVR--LSTLA-RLF-GATTTPTHRAL 165
|
....*....
gi 2087741084 158 LDAEILADV 166
Cdd:PRK07883 166 DDARATVDV 174
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
4-164 |
1.55e-23 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 94.74 E-value: 1.55e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSGHRIIEIGCVELINRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:PRK07740 62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGA 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 84 AELVIHNAPFDVGFIDSELKRLGSPRWQNVathcgVLDTLALAR-EKHPGQKNNLDALCKRYFVDNSQRdlHGALLDAEI 162
Cdd:PRK07740 142 GVLVAHHAGHDKAFLRHALWRTYRQPFTHR-----LIDTMFLTKlLAHERDFPTLDDALAYYGIPIPRR--HHALGDALM 214
|
..
gi 2087741084 163 LA 164
Cdd:PRK07740 215 TA 216
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
5-166 |
1.65e-19 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 85.14 E-value: 1.65e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLDPkSGHRIIEIGCVELINRKLTGRHYHQYINPEreVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK06063 19 VVDVETSGFRP-GQARIISLAVLGLDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGR 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 85 ELVIHNAPFDVGFIDSELKRLGS--PRWQnvathcgVLDTLALAREKHPGQKN-NLDALCKRYFVdnSQRDLHGALLDAE 161
Cdd:PRK06063 96 TLVAHNVAFDYSFLAAEAERAGAelPVDQ-------VMCTVELARRLGLGLPNlRLETLAAHWGV--PQQRPHDALDDAR 166
|
....*
gi 2087741084 162 ILADV 166
Cdd:PRK06063 167 VLAGI 171
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
4-168 |
9.58e-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: 79.86 E-value: 9.58e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSghrIIEIGCVELINRKLTGRHYHqYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:cd06130 2 VAIDFETANADRAS---ACSIGLVKVRDGQIVDTFYT-LIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 84 AELVIHNAPFDVGFIDSELKR--LGSPRWQnvathcgVLDTLALAREKHPGQKN-NLDALCKRYFVDnsqRDLHGALLDA 160
Cdd:cd06130 78 SLVVAHNASFDRSVLRAALEAygLPPPPYQ-------YLCTVRLARRVWPLLPNhKLNTVAEHLGIE---LNHHDALEDA 147
|
....*...
gi 2087741084 161 EILADVYL 168
Cdd:cd06130 148 RACAEILL 155
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
4-167 |
1.33e-18 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 81.80 E-value: 1.33e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVEL-INRKLTGrhYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC- 81
Cdd:PRK06310 10 VCLDCETTGLDVKK-DRIIEFAAIRFtFDEVIDS--VEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFk 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DGAELVIHNAPFDVGFIDSELKRLGSPRwqnVATHCGVLDTLALAREKHPGQKNNLDALCKRYFVDNSQRdlHGALLDAE 161
Cdd:PRK06310 87 EGDYIVGHSVGFDLQVLSQESERIGETF---LSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN--HRAMKDVE 161
|
....*.
gi 2087741084 162 ILADVY 167
Cdd:PRK06310 162 INIKVF 167
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
2-172 |
3.10e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 74.85 E-value: 3.10e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 2 RQIVLDTETTGLDPKSgHRIIEIGCVELInrklTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFC 81
Cdd:PRK06309 3 ALIFYDTETTGTQIDK-DRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 82 DG-AELVIHNA-PFDVGFIDSELKR--LGSPRWQnvathcgVLDTLALAREKHPG-QKNNLDALCKRYFVDNSQRdlHGA 156
Cdd:PRK06309 78 GTdNILVAHNNdAFDFPLLRKECRRhgLEPPTLR-------TIDSLKWAQKYRPDlPKHNLQYLRQVYGFEENQA--HRA 148
|
170
....*....|....*.
gi 2087741084 157 LLDAEILADVYLIMTG 172
Cdd:PRK06309 149 LDDVITLHRVFSALVG 164
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
5-163 |
2.96e-15 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 72.75 E-value: 2.96e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLDPKsGHRIIEIGCVELINRKLTGRhYHQYINPErEVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK08517 72 FVDIETNGSKPK-KHQIIEIGAVKVKNGEIIDR-FESFVKAK-EVPEYITELTGITYEDLENAPSLKEVLEEFRLFLGDS 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 85 ELVIHNAPFDVGFIDSELKRLGSPRWQNVAthcgvLDTLALAREKHPGQKNNLDALcKRYF---VDNSQRDLHGALLDAE 161
Cdd:PRK08517 149 VFVAHNVNFDYNFISRSLEEIGLGPLLNRK-----LCTIDLAKRTIESPRYGLSFL-KELLgieIEVHHRAYADALAAYE 222
|
..
gi 2087741084 162 IL 163
Cdd:PRK08517 223 IF 224
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
4-105 |
8.64e-14 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 67.62 E-value: 8.64e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVELI-NRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCD 82
Cdd:PRK09145 32 VALDCETTGLDPRR-AEIVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIG 110
|
90 100
....*....|....*....|...
gi 2087741084 83 GAELVIHNAPFDVGFIDSELKRL 105
Cdd:PRK09145 111 NRPLVGYYLEFDVAMLNRYVRPL 133
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
4-160 |
1.23e-13 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 67.69 E-value: 1.23e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSGhRIIEiGCVELINRKLTGRHYHQYI-NPEREVDDGAIEVHGITNEFLVD--KPIfSQVVDEFMT- 79
Cdd:PRK07942 9 AAFDLETTGVDPETA-RIVT-AALVVVDADGEVVESREWLaDPGVEIPEEASAVHGITTEYARAhgRPA-AEVLAEIADa 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 80 ----FCDGAELVIHNAPFDVGFIDSELKRLGSPrwQNVATHcgVLDTLALAREKHPGQ--KNNLDALCKRYFV--DNSqr 151
Cdd:PRK07942 86 lreaWARGVPVVVFNAPYDLTVLDRELRRHGLP--SLVPGP--VIDPYVIDKAVDRYRkgKRTLTALCEHYGVrlDNA-- 159
|
....*....
gi 2087741084 152 dlHGALLDA 160
Cdd:PRK07942 160 --HEATADA 166
|
|
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
6-134 |
4.67e-13 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 66.49 E-value: 4.67e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 6 LDTETTGLDPKSgHRIIEIGCVEL-INRKLTGRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK09146 52 LDFETTGLDAEQ-DAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGK 130
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 2087741084 85 ELVIHNAPFDVGFIDSELK-RLGSPrwqnvaTHCGVLDTLALAREKHPGQK 134
Cdd:PRK09146 131 VVVVHYRRIERDFLDQALRnRIGEG------IEFPVIDTMEIEARIQRKQA 175
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
4-104 |
2.93e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 62.15 E-value: 2.93e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSGhRIIEIGCVELINRKLTGRHYHQYINPERevDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDG 83
Cdd:PRK05601 49 VAVSIQTSGIHPSTS-RLITIDAVTLTADGEEVEHFHAVLNPGE--DPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDG 125
|
90 100
....*....|....*....|.
gi 2087741084 84 AELVIHNAPFDVGFIDSELKR 104
Cdd:PRK05601 126 RTLILHNAPRTWGFIVSEAKR 146
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
4-99 |
5.29e-11 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 61.14 E-value: 5.29e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVeLINRKLTGR------HYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEF 77
Cdd:PRK09182 40 VILDTETTGLDPRK-DEIIEIGMV-AFEYDDDGRigdvldTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAAVDAL 117
|
90 100
....*....|....*....|...
gi 2087741084 78 MtfcDGAELVI-HNAPFDVGFID 99
Cdd:PRK09182 118 I---APADLIIaHNAGFDRPFLE 137
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
5-94 |
9.35e-10 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 56.65 E-value: 9.35e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLdpKSGhrIIEIGCVELINRKLTGRHYHqYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMtfcdGA 84
Cdd:PRK07983 4 VIDTETCGL--QGG--IVEIASVDVIDGKIVNPMSH-LVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYY----GS 74
|
90
....*....|.
gi 2087741084 85 EL-VIHNAPFD 94
Cdd:PRK07983 75 EWyVAHNASFD 85
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
5-168 |
1.73e-09 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 57.39 E-value: 1.73e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 5 VLDTETTGLDPKSghRIIEIGCVELINRKLTgRHYHQYINPEREVDDGAIEVHGITNEFLVDKPIFSQVVDEFMTFCDGA 84
Cdd:PRK07246 11 VVDLEATGAGPNA--SIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 85 ELVIHNAPFDVGFIDSEL----KRLGSPRwqnvathcgvLDTLALAREKHPG-QKNNLDALCKRYFVDNSqrDLHGALLD 159
Cdd:PRK07246 88 IFVAHNVKFDANLLAEALflegYELRTPR----------VDTVELAQVFFPTlEKYSLSHLSRELNIDLA--DAHTAIAD 155
|
....*....
gi 2087741084 160 AEILADVYL 168
Cdd:PRK07246 156 ARATAELFL 164
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
4-167 |
2.95e-07 |
|
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Pssm-ID: 99837 [Multi-domain] Cd Length: 189 Bit Score: 49.21 E-value: 2.95e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSgHRIIEIGCVEL-INRK---LTGRHYHQYINPER--EVDDGAIEVHGI---------TNEFLVDKP 68
Cdd:cd06134 8 VVVDVETGGFNPQT-DALLEIAAVTLeMDEQgnlYPDETFHFHILPFEgaNLDPAALEFNGIdpfhpfrfaVDEKEALKE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 69 IFSQVVDEF-MTFCDGAELVIHNAPFDVGFIDSELKRLGSPRwqNVATHCGVLDTLALAREKHpGQkNNLDALCKRYFVD 147
Cdd:cd06134 87 IFKPIRKALkAQGCTRAILVGHNAHFDLGFLNAAVARCKIKR--NPFHPFSTFDTATLAGLAY-GQ-TVLAKACQAAGIE 162
|
170 180
....*....|....*....|
gi 2087741084 148 NSQRDLHGALLDAEILADVY 167
Cdd:cd06134 163 FDNKEAHSALYDTQKTAELF 182
|
|
| TREX1_2 |
cd06136 |
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ... |
4-145 |
3.79e-07 |
|
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: 48.87 E-value: 3.79e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLDPKSGHRIIEIgCVELINRKLTGRHYHQY-------------INPEREVDDGAIEVHGITNEFLVDKPIF 70
Cdd:cd06136 2 VFLDLETTGLPKHNRPEITEL-CLVAVHRDHLLNTSRDKpalprvldklslcFNPGRAISPGASEITGLSNDLLEHKAPF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 71 -SQVVDEFMTFCDGAE----LVIHNA-PFDVGFIDSELKRLGSPRWQNvaTHCgvLDTLALAREKHpgqkNNLDALCKRY 144
Cdd:cd06136 81 dSDTANLIKLFLRRQPkpicLVAHNGnRFDFPILRSELERLGTKLPDD--ILC--VDSLPAFRELD----QSLGSLYKRL 152
|
.
gi 2087741084 145 F 145
Cdd:cd06136 153 F 153
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
4-81 |
6.21e-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: 47.99 E-value: 6.21e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 4 IVLDTETTGLD----PKSGHRIIEIGCVEL-INRKLTGRHYHQYINPER--EVDDGAIEVHGITNEFLVDKPIFSQVVDE 76
Cdd:cd06133 2 LVIDFEATCWEgnskPDYPNEIIEIGAVLVdVKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKE 81
|
....*
gi 2087741084 77 FMTFC 81
Cdd:cd06133 82 FLEWL 86
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
2-78 |
7.09e-04 |
|
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: 40.08 E-value: 7.09e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2087741084 2 RQIVLDTETTGLDPKSgHRIIEIGCVELINRKLTGRHYHQYINPEREVDDgAIEVHGITNEFLVDKPI-FSQVVDEFM 78
Cdd:pfam13361 187 NIVVFDVETTGLDTTE-DEIIQIAAIKLNKKGVVIESFERFLRLKKPVGD-SLQVHGFSDEFLQENGEtPAEALRDFL 262
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
6-112 |
8.43e-04 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 38.73 E-value: 8.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 6 LDTETTGLDPKSGHrIIEIGCveLINRKLTGRHYHQYINPEREvDDGAIEvhgitneflvdkpifsqvvDEFMTFCDGAE 85
Cdd:pfam13482 3 FDIETTGLSPGKNT-IYLIGV--YDVDGDKVRTFVQYLAEGPT-EEAAIL-------------------QLFELLADYPL 59
|
90 100
....*....|....*....|....*...
gi 2087741084 86 LVIHN-APFDVGFIDSELKRLGSPRWQN 112
Cdd:pfam13482 60 LVTFNgKSFDVPFIKRRFKRYDLDELFR 87
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
54-135 |
9.87e-04 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 39.76 E-value: 9.87e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087741084 54 IEVHGITNEFLVDKPIFSQVVDEFMTFCDGAELVIHNAPFDVGFIDS--ELKRLGSPRWQNVathCgvldTLALAREKHP 131
Cdd:PRK06195 51 IGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKtlELYNIPMPSFEYI---C----TMKLAKNFYS 123
|
....
gi 2087741084 132 GQKN 135
Cdd:PRK06195 124 NIDN 127
|
|
| Orn |
cd06135 |
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ... |
6-27 |
1.30e-03 |
|
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Pssm-ID: 99838 [Multi-domain] Cd Length: 173 Bit Score: 38.30 E-value: 1.30e-03
|
| PRK05359 |
PRK05359 |
oligoribonuclease; Provisional |
4-27 |
3.62e-03 |
|
oligoribonuclease; Provisional
Pssm-ID: 235429 Cd Length: 181 Bit Score: 37.06 E-value: 3.62e-03
|
| Orn |
COG1949 |
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]; |
6-27 |
6.42e-03 |
|
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
Pssm-ID: 441552 Cd Length: 177 Bit Score: 36.24 E-value: 6.42e-03
|
| |
