|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
3-178 |
7.12e-78 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 230.80 E-value: 7.12e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 3 QANSVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSE 82
Cdd:COG2176 6 EDLTYVVFDLETTGLSPK-KDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 83 FIAGENLIAHNASFDKRFLDAELERIHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDgVFHRALADAQMTAK 162
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLE-DRHRALGDAEATAE 163
|
170
....*....|....*.
gi 1219744296 163 LWLLMVEELQHSGIAN 178
Cdd:COG2176 164 LFLKLLEKLEEKGITT 179
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
8-165 |
9.68e-57 |
|
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: 176.72 E-value: 9.68e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNG-EVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:cd06127 1 VVFDTETTGLDPK-KDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIHCGY-SGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQMTAKLWL 165
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPlPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAELLL 159
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
8-176 |
2.01e-51 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 173.57 E-value: 2.01e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK07883 18 VVVDLETTGGSPA-GDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 88 NLIAHNASFDKRFLDAELERihCGY---SGEFACSLLVARRLI--QDAPSHKLGELVRYKNIDNDGVfHRALADAQMTAK 162
Cdd:PRK07883 97 VLVAHNAPFDIGFLRAAAAR--CGYpwpGPPVLCTVRLARRVLprDEAPNVRLSTLARLFGATTTPT-HRALDDARATVD 173
|
170
....*....|....
gi 1219744296 163 LWLLMVEELQHSGI 176
Cdd:PRK07883 174 VLHGLIERLGNLGV 187
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
6-171 |
1.82e-45 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 148.22 E-value: 1.82e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 6 SVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIA 85
Cdd:smart00479 1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 86 GENLIAHN-ASFDKRFLDAELER--IHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQMTAK 162
Cdd:smart00479 80 GRILVAGNsAHFDLRFLKLEHPRlgIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAK 159
|
....*....
gi 1219744296 163 LWLLMVEEL 171
Cdd:smart00479 160 LFKKLLERL 168
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
8-163 |
2.76e-35 |
|
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: 122.07 E-value: 2.76e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGE--VVETFQQLMNP--GFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEF 83
Cdd:pfam00929 1 VVIDLETTGLDPE-KDEIIEIAAVVIDGGEneIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 84 IAGEN-LIAHNASFDKRFLDAELERI---HCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQM 159
Cdd:pfam00929 80 LRKGNlLVAHNASFDVGFLRYDDKRFlkkPMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRAHRALDDARA 159
|
....
gi 1219744296 160 TAKL 163
Cdd:pfam00929 160 TAKL 163
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
8-169 |
1.50e-22 |
|
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: 90.59 E-value: 1.50e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLspNLGDRAIEIGAVKLVNG-EVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:TIGR00573 10 TTGDNETTGL--YAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIH--CGYSGEFACSLLVARRLIQDAPSHKLGEL---VRYKNIDNDGVFHRALADAQMTA 161
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKLYkvEPKTNDVIDTTDTLQYARPEFPGKRNTLDalcKRYEITNSHRALHGALADAFILA 167
|
....*...
gi 1219744296 162 KLWLLMVE 169
Cdd:TIGR00573 168 KLYLVMTG 175
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
3-178 |
7.12e-78 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 230.80 E-value: 7.12e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 3 QANSVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSE 82
Cdd:COG2176 6 EDLTYVVFDLETTGLSPK-KDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 83 FIAGENLIAHNASFDKRFLDAELERIHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDgVFHRALADAQMTAK 162
Cdd:COG2176 85 FLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLE-DRHRALGDAEATAE 163
|
170
....*....|....*.
gi 1219744296 163 LWLLMVEELQHSGIAN 178
Cdd:COG2176 164 LFLKLLEKLEEKGITT 179
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
7-169 |
4.67e-61 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 187.69 E-value: 4.67e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 7 VVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:COG0847 2 FVVLDTETTGLDPA-KDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIHCGYSG-EFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGvFHRALADAQMTAKLWL 165
Cdd:COG0847 81 AVLVAHNAAFDLGFLNAELRRAGLPLPPfPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDE-RHRALADAEATAELFL 159
|
....
gi 1219744296 166 LMVE 169
Cdd:COG0847 160 ALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
8-165 |
9.68e-57 |
|
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: 176.72 E-value: 9.68e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNG-EVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:cd06127 1 VVFDTETTGLDPK-KDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIHCGY-SGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQMTAKLWL 165
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPlPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAELLL 159
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
8-176 |
2.01e-51 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 173.57 E-value: 2.01e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK07883 18 VVVDLETTGGSPA-GDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 88 NLIAHNASFDKRFLDAELERihCGY---SGEFACSLLVARRLI--QDAPSHKLGELVRYKNIDNDGVfHRALADAQMTAK 162
Cdd:PRK07883 97 VLVAHNAPFDIGFLRAAAAR--CGYpwpGPPVLCTVRLARRVLprDEAPNVRLSTLARLFGATTTPT-HRALDDARATVD 173
|
170
....*....|....
gi 1219744296 163 LWLLMVEELQHSGI 176
Cdd:PRK07883 174 VLHGLIERLGNLGV 187
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
8-178 |
1.16e-47 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 166.94 E-value: 1.16e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLgDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK00448 422 VVFDVETTGLSAVY-DEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 88 NLIAHNASFDKRFLDAELERIhcgYSGEFAC----SLLVARRLIQDAPSHKLGELVRYKNI--DNDgvfHRALADAQMTA 161
Cdd:PRK00448 501 ILVAHNASFDVGFINTNYEKL---GLEKIKNpvidTLELSRFLYPELKSHRLNTLAKKFGVelEHH---HRADYDAEATA 574
|
170
....*....|....*..
gi 1219744296 162 KLWLLMVEELQHSGIAN 178
Cdd:PRK00448 575 YLLIKFLKDLKEKGITN 591
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
6-171 |
1.82e-45 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 148.22 E-value: 1.82e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 6 SVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIA 85
Cdd:smart00479 1 TLVVIDCETTGLDPG-KDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 86 GENLIAHN-ASFDKRFLDAELER--IHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQMTAK 162
Cdd:smart00479 80 GRILVAGNsAHFDLRFLKLEHPRlgIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDDARATAK 159
|
....*....
gi 1219744296 163 LWLLMVEEL 171
Cdd:smart00479 160 LFKKLLERL 168
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
8-167 |
4.14e-40 |
|
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: 134.58 E-value: 4.14e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLGDRAIEIGAVKLVNGEVV-ETFQQLMNPGFRVSSfiESY--TGITNNMLRSAPSCDEVMASFSEFI 84
Cdd:cd06131 2 IVLDTETTGLDPREGHRIIEIGCVELINRRLTgNTFHVYINPERDIPE--EAFkvHGITDEFLADKPKFAEIADEFLDFI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 85 AGENLIAHNASFDKRFLDAELERIHCG----YSGEFACSLLVARRLIQDAPsHKLGELVRYKNIDNDG-VFHRALADAQM 159
Cdd:cd06131 80 RGAELVIHNASFDVGFLNAELSLLGLGkkiiDFCRVIDTLALARKKFPGKP-NSLDALCKRFGIDNSHrTLHGALLDAEL 158
|
....*...
gi 1219744296 160 TAKLWLLM 167
Cdd:cd06131 159 LAEVYLEL 166
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
8-173 |
5.26e-40 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 144.71 E-value: 5.26e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK08074 6 VVVDLETTGNSPKKGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 88 NLIAHNASFDKRFLDAELERihCGYSgEFACSLL----VARRLIQDAPSHKLGELVRYKNIDNDGVfHRALADAQMTAKL 163
Cdd:PRK08074 86 YFVAHNVHFDLNFLNEELER--AGYT-EIHCPKLdtveLARILLPTAESYKLRDLSEELGLEHDQP-HRADSDAEVTAEL 161
|
170
....*....|
gi 1219744296 164 WLLMVEELQH 173
Cdd:PRK08074 162 FLQLLNKLER 171
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
6-176 |
9.68e-39 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 133.26 E-value: 9.68e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 6 SVVVLDFETTGLSPNLGDRAIEIGAVKLVNGEVV-ETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFI 84
Cdd:PRK07740 60 PFVVFDLETTGFSPQQGDEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFI 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 85 AGENLIAHNASFDKRFLDAELER-IHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVfHRALADAQMTAKL 163
Cdd:PRK07740 140 GAGVLVAHHAGHDKAFLRHALWRtYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRR-HHALGDALMTAKL 218
|
170
....*....|...
gi 1219744296 164 WLLMVEELQHSGI 176
Cdd:PRK07740 219 WAILLVEAQQRGI 231
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
8-165 |
4.47e-38 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 133.40 E-value: 4.47e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPnLGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK06807 11 VVIDFETTGFNP-YNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1219744296 88 NLIAHNASFDKRFLDAELERIHCGYSGEFAC-SLLVARRLIQDAPSHKLGELVRYKNIDNDGvfHRALADAQMTAKLWL 165
Cdd:PRK06807 90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIdTVFLAKKYMKHAPNHKLETLKRMLGIRLSS--HNAFDDCITCAAVYQ 166
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
8-163 |
2.76e-35 |
|
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: 122.07 E-value: 2.76e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGE--VVETFQQLMNP--GFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEF 83
Cdd:pfam00929 1 VVIDLETTGLDPE-KDEIIEIAAVVIDGGEneIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 84 IAGEN-LIAHNASFDKRFLDAELERI---HCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVFHRALADAQM 159
Cdd:pfam00929 80 LRKGNlLVAHNASFDVGFLRYDDKRFlkkPMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRAHRALDDARA 159
|
....
gi 1219744296 160 TAKL 163
Cdd:pfam00929 160 TAKL 163
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
8-163 |
2.65e-29 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 109.34 E-value: 2.65e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFrVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGE 87
Cdd:PRK08517 71 CFVDIETNGSKPK-KHQIIEIGAVKVKNGEIIDRFESFVKAKE-VPEYITELTGITYEDLENAPSLKEVLEEFRLFLGDS 148
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1219744296 88 NLIAHNASFDKRFLDAELERI-HCGYSGEFACSLLVARRLIQdAPSHKLGELVRYKNIDNDgVFHRALADAQMTAKL 163
Cdd:PRK08517 149 VFVAHNVNFDYNFISRSLEEIgLGPLLNRKLCTIDLAKRTIE-SPRYGLSFLKELLGIEIE-VHHRAYADALAAYEI 223
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
8-165 |
6.20e-29 |
|
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: 105.29 E-value: 6.20e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETtglsPNlGDR--AIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIA 85
Cdd:cd06130 2 VAIDFET----AN-ADRasACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 86 GENLIAHNASFDKRFLDAELERIHCGY-SGEFACSLLVARRLIQDAPSHKLGELVRYKNIDndgvF--HRALADAQMTAK 162
Cdd:cd06130 77 GSLVVAHNASFDRSVLRAALEAYGLPPpPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIE----LnhHDALEDARACAE 152
|
...
gi 1219744296 163 LWL 165
Cdd:cd06130 153 ILL 155
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
8-167 |
7.77e-27 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 102.24 E-value: 7.77e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLGDRAIEIGAVKLVN----GEvveTFQQLMNPGfRVSSFiESY--TGITNNMLRSAPSCDEVMASFS 81
Cdd:PRK05711 7 IVLDTETTGLNQREGHRIIEIGAVELINrrltGR---NFHVYIKPD-RLVDP-EALavHGITDEFLADKPTFAEVADEFL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 82 EFIAGENLIAHNASFDKRFLDAELERIHCGYsGEFA--C----SLLVARRLIQDAPsHKLGELV-RYKnIDNDG-VFHRA 153
Cdd:PRK05711 82 DFIRGAELIIHNAPFDIGFMDYEFALLGRDI-PKTNtfCkvtdTLAMARRMFPGKR-NSLDALCkRYG-IDNSHrTLHGA 158
|
170
....*....|....
gi 1219744296 154 LADAQMTAKLWLLM 167
Cdd:PRK05711 159 LLDAEILAEVYLAM 172
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
5-172 |
2.60e-23 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 91.46 E-value: 2.60e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 5 NSVVVLDFETTGlSPNLGDRA-----IEIGAVKL-VNGEVVETFQQLMNPGFR--VSSFIESYTGITNNMLRSAPSCDEV 76
Cdd:COG5018 2 MKYLVIDLEATC-WDGKPPPGfpmeiIEIGAVKVdENGEIIDEFSSFVKPVRRpkLSPFCTELTGITQEDVDSAPSFAEA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 77 MASFSEFIAGEN-LIAHNASFDKRFLDAELERIHCGYS-GEFACSLLVARRLIQDAPSH-KLGELVRYKNIDNDGVFHRA 153
Cdd:COG5018 81 IEDFKKWIGSEDyILCSWGDYDRKQLERNCRFHGVPYPfGDRHINLKKLFALYFGLKKRiGLKKALELLGLEFEGTHHRA 160
|
170
....*....|....*....
gi 1219744296 154 LADAQMTAKLWLLMVEELQ 172
Cdd:COG5018 161 LDDARNTAKLFKKILGDKR 179
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
8-169 |
1.50e-22 |
|
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: 90.59 E-value: 1.50e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLspNLGDRAIEIGAVKLVNG-EVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:TIGR00573 10 TTGDNETTGL--YAGHDIIEIGAVEIINRrITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIH--CGYSGEFACSLLVARRLIQDAPSHKLGEL---VRYKNIDNDGVFHRALADAQMTA 161
Cdd:TIGR00573 88 AELVIHNASFDVGFLNYEFSKLYkvEPKTNDVIDTTDTLQYARPEFPGKRNTLDalcKRYEITNSHRALHGALADAFILA 167
|
....*...
gi 1219744296 162 KLWLLMVE 169
Cdd:TIGR00573 168 KLYLVMTG 175
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
8-163 |
2.09e-21 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 89.37 E-value: 2.09e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKL-VNGEVVETFQQLMNPGfrVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:PRK06063 18 AVVDVETSGFRPG-QARIISLAVLGLdADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRG 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIHCGYSGEFA-CSLLVARRLIQDAPSHKLGELVRYKnidndGVF----HRALADAQMTA 161
Cdd:PRK06063 95 RTLVAHNVAFDYSFLAAEAERAGAELPVDQVmCTVELARRLGLGLPNLRLETLAAHW-----GVPqqrpHDALDDARVLA 169
|
..
gi 1219744296 162 KL 163
Cdd:PRK06063 170 GI 171
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
7-167 |
4.75e-18 |
|
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: 77.65 E-value: 4.75e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 7 VVVLDFETT----GLSPNLGDRAIEIGAVKLV--NGEVVETFQQL----MNPgfRVSSFIESYTGITNNMLRSAPSCDEV 76
Cdd:cd06133 1 YLVIDFEATcwegNSKPDYPNEIIEIGAVLVDvkTKEIIDTFSSYvkpvINP--KLSDFCTELTGITQEDVDNAPSFPEV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 77 MASFSEFIaGENLIAHNASF---DkrflDAELERIHCGYSGEFACSLL--------VARRLIQDAPSHKLGELVRYKNID 145
Cdd:cd06133 79 LKEFLEWL-GKNGKYAFVTWgdwD----LKDLLQNQCKYKIINLPPFFrqwidlkkEFAKFYGLKKRTGLSKALEYLGLE 153
|
170 180
....*....|....*....|..
gi 1219744296 146 NDGVFHRALADAQMTAKLWLLM 167
Cdd:cd06133 154 FEGRHHRGLDDARNIARILKRL 175
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
6-166 |
8.50e-18 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 79.25 E-value: 8.50e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 6 SVVVLDFETTGLSPNlGDRAIEIGAVKLVN------GEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSApSCDevMAS 79
Cdd:PRK09182 38 LGVILDTETTGLDPR-KDEIIEIGMVAFEYdddgriGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQ-TID--PAA 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 80 FSEFIAGENL-IAHNASFDKRFLDAelerihcgYSGEF-----ACSLlvarrliQDAP-------SHKLGELVRYKNIDN 146
Cdd:PRK09182 114 VDALIAPADLiIAHNAGFDRPFLER--------FSPVFatkpwACSV-------SEIDwsargfeGTKLGYLAGQAGFFH 178
|
170 180
....*....|....*....|
gi 1219744296 147 DGvfHRALADAQmtAKLWLL 166
Cdd:PRK09182 179 EG--HRAVDDCQ--ALLELL 194
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
5-164 |
3.20e-17 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 77.18 E-value: 3.20e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 5 NSVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFI 84
Cdd:PRK06310 7 TEFVCLDCETTGLDVK-KDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 85 A-GENLIAHNASFDKRFLDAELER--IHCGYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVfHRALADAQMTA 161
Cdd:PRK06310 86 KeGDYIVGHSVGFDLQVLSQESERigETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGN-HRAMKDVEINI 164
|
...
gi 1219744296 162 KLW 164
Cdd:PRK06310 165 KVF 167
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
11-171 |
1.44e-16 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 74.85 E-value: 1.44e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 11 DFETTGLSPNlGDRAIEIGAVKLVNGEvveTFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGEN-L 89
Cdd:PRK06309 8 DTETTGTQID-KDRIIEIAAYNGVTSE---SFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNiL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 90 IAHNA-SFDKRFLDAELERiHC--GYSGEFACSLLVARRLIQDAPSHKLGELVRYKNIDNDGVfHRALADAQMTAKLWLL 166
Cdd:PRK06309 84 VAHNNdAFDFPLLRKECRR-HGlePPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQA-HRALDDVITLHRVFSA 161
|
....*
gi 1219744296 167 MVEEL 171
Cdd:PRK06309 162 LVGDL 166
|
|
| PRK06195 |
PRK06195 |
DNA polymerase III subunit epsilon; Validated |
8-171 |
1.50e-15 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235735 [Multi-domain] Cd Length: 309 Bit Score: 73.28 E-value: 1.50e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlgdRAIEIGAVKLVNGEVVETFQQLMNPG-FRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:PRK06195 4 VAIDFETANEKRN---SPCSIGIVVVKDGEIVEKVHYLIKPKeMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 ENLIAHNASFDKRFLDAELERIHCGY-SGEFACSLLVARRLIQDAPSHKLGEL-----VRYKNidndgvfHRALADAQMT 160
Cdd:PRK06195 81 NLVIAHNASFDISVLRKTLELYNIPMpSFEYICTMKLAKNFYSNIDNARLNTVnnflgYEFKH-------HDALADAMAC 153
|
170
....*....|.
gi 1219744296 161 AKLWLLMVEEL 171
Cdd:PRK06195 154 SNILLNISKEL 164
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
5-165 |
1.21e-13 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 68.95 E-value: 1.21e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 5 NSVVVLDFETTGLSPNLgdRAIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFI 84
Cdd:PRK07246 7 RKYAVVDLEATGAGPNA--SIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 85 AGENLIAHNASFDKRFLdAE---LErihcGYsgefacSLLVAR----RLIQ----DAPSHKLGELVRYKNID-NDGvfHR 152
Cdd:PRK07246 85 EDCIFVAHNVKFDANLL-AEalfLE----GY------ELRTPRvdtvELAQvffpTLEKYSLSHLSRELNIDlADA--HT 151
|
170
....*....|...
gi 1219744296 153 ALADAQMTAKLWL 165
Cdd:PRK07246 152 AIADARATAELFL 164
|
|
| PRK07983 |
PRK07983 |
exodeoxyribonuclease X; Provisional |
9-169 |
1.22e-13 |
|
exodeoxyribonuclease X; Provisional
Pssm-ID: 181186 [Multi-domain] Cd Length: 219 Bit Score: 66.67 E-value: 1.22e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 9 VLDFETTGLSPNLgdraIEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASF--SEFiag 86
Cdd:PRK07983 4 VIDTETCGLQGGI----VEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYygSEW--- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 87 enLIAHNASFDKRFldaeLERIHcgysGEFACSLLVARRLIqdaPSHKLGELVRYK----NIDN-DGVF-HRALADAQMT 160
Cdd:PRK07983 77 --YVAHNASFDRRV----LPEMP----GEWICTMKLARRLW---PGIKYSNMALYKsrklNVQTpPGLHhHRALYDCYIT 143
|
....*....
gi 1219744296 161 AKLWLLMVE 169
Cdd:PRK07983 144 AALLIDIMN 152
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
1-167 |
5.67e-11 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 59.15 E-value: 5.67e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 1 MPQANSVVVLDFETTGLSPNlGDRAIEIGAVKLVNGEVV--ETFQQLMNPGFRVSSfiESYT--GITNNMLRSAPSCDEV 76
Cdd:PRK09145 25 PPPPDEWVALDCETTGLDPR-RAEIVSIAAVKIRGNRILtsERLELLVRPPQSLSA--ESIKihRLRHQDLEDGLSEEEA 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 77 MASFSEFIAGENLIAHNASFDKRFLDAELERiHCGY---SGEFACSLLVARRLIQDAP----SHKLGELVRYKNIDNDGV 149
Cdd:PRK09145 102 LRQLLAFIGNRPLVGYYLEFDVAMLNRYVRP-LLGIplpNPLIEVSALYYDKKERHLPdayiDLRFDAILKHLDLPVLGR 180
|
170
....*....|....*...
gi 1219744296 150 fHRALADAQMTAKLWLLM 167
Cdd:PRK09145 181 -HDALNDAIMAALIFLRL 197
|
|
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
1-170 |
6.80e-09 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 54.29 E-value: 6.80e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 1 MPQANSVVVLDFETTgLSPNLGD---RAIEIGAVKLVNG--EVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDE 75
Cdd:PRK06722 1 MENATHFIVFDIERN-FRPYKSEdpsEIVDIGAVKIEAStmKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQ 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 76 VMASFSEFIAGENLIAHNASFDKRFL--DAELERIHC---GYSGEFACSLLVAR---RLIQDAPShkLGELVRYKNIDND 147
Cdd:PRK06722 80 IIEKFIQFIGEDSIFVTWGKEDYRFLshDCTLHSVECpcmEKERRIDLQKFVFQayeELFEHTPS--LQSAVEQLGLIWE 157
|
170 180
....*....|....*....|...
gi 1219744296 148 GVFHRALADAQMTAKLWLLMVEE 170
Cdd:PRK06722 158 GKQHRALADAENTANILLKAYSE 180
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
26-94 |
1.27e-08 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 52.48 E-value: 1.27e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1219744296 26 IEIGAVKLVNGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGENLIAHNA 94
Cdd:PRK07247 24 IQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFVGELPLIGYNA 92
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
6-163 |
7.87e-07 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 48.05 E-value: 7.87e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 6 SVVVLDFETTGLSPnLGDRaIEIGAVKLV--NGEVVETFQQLMNPGFRVSSFIESYTGITNNMLRS--APScDEVMASFS 81
Cdd:PRK07942 7 PLAAFDLETTGVDP-ETAR-IVTAALVVVdaDGEVVESREWLADPGVEIPEEASAVHGITTEYARAhgRPA-AEVLAEIA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 82 E-----FIAGENLIAHNASFDKRFLDAELERIHcgysGEFACSLLVARRLIQDAPSHK-------LGELVRYKNIDNDGV 149
Cdd:PRK07942 84 DalreaWARGVPVVVFNAPYDLTVLDRELRRHG----LPSLVPGPVIDPYVIDKAVDRyrkgkrtLTALCEHYGVRLDNA 159
|
170
....*....|....
gi 1219744296 150 fHRALADAQMTAKL 163
Cdd:PRK07942 160 -HEATADALAAARV 172
|
|
| PRK05601 |
PRK05601 |
DNA polymerase III subunit epsilon; Validated |
8-107 |
8.02e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 235529 [Multi-domain] Cd Length: 377 Bit Score: 45.59 E-value: 8.02e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLGdRAIEIGAVKL-VNGEVVETFQQLMNPGFRVSSFieSYTGITNNMLRSAPSCDEVMASFSEFIAG 86
Cdd:PRK05601 49 VAVSIQTSGIHPSTS-RLITIDAVTLtADGEEVEHFHAVLNPGEDPGPF--HLHGLSAEEFAQGKRFSQILKPLDRLIDG 125
|
90 100
....*....|....*....|.
gi 1219744296 87 ENLIAHNASFDKRFLDAELER 107
Cdd:PRK05601 126 RTLILHNAPRTWGFIVSEAKR 146
|
|
| RNaseT |
cd06134 |
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ... |
8-168 |
8.80e-05 |
|
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: 41.51 E-value: 8.80e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNlGDRAIEIGAVKLVNGE-----VVETFQQLMNPgFRVSSFIES---YTGIT-NNMLRSAPSCDEVMA 78
Cdd:cd06134 8 VVVDVETGGFNPQ-TDALLEIAAVTLEMDEqgnlyPDETFHFHILP-FEGANLDPAaleFNGIDpFHPFRFAVDEKEALK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 79 SFSEFIAGEN---------LIAHNASFDKRFLDAELERihCGYSG----EFAC---SLLVARRLIQDApshkLGELVRYK 142
Cdd:cd06134 86 EIFKPIRKALkaqgctraiLVGHNAHFDLGFLNAAVAR--CKIKRnpfhPFSTfdtATLAGLAYGQTV----LAKACQAA 159
|
170 180
....*....|....*....|....*..
gi 1219744296 143 NID-NDGVFHRALADAQMTAKLWLLMV 168
Cdd:cd06134 160 GIEfDNKEAHSALYDTQKTAELFCKIV 186
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
8-164 |
3.10e-04 |
|
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.
Pssm-ID: 406788 Cd Length: 177 Bit Score: 39.72 E-value: 3.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 8 VVLDFETTGLSPNLgdrAI-EIGAVK--LVNGEVVETFQQLMNP------GFRVSSFIESYTGITNNMLRS------APS 72
Cdd:pfam16473 3 LMIDIETLGNEPTA---PIvSIGAVFfdPETGELGKEFYARIDLessmsaGATIDADTILWWLKQSSEARAqllgddAPS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 73 CDEVMASFSEFIA------GENLIAHNASFDKRFLDAELERIHCGYSGEFACSLLVaRRLIQDAPshKLGELVRYKnIDN 146
Cdd:pfam16473 80 LPDALLDLNDFIRdngdpkSLKVWGNGASFDNVILRAAFERGGLPAPWKYWNDRDV-RTIVALGP--ELGYDPKRD-IPF 155
|
170
....*....|....*...
gi 1219744296 147 DGVFHRALADAQMTAKLW 164
Cdd:pfam16473 156 EGVKHNALDDAIHQAKYV 173
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
4-84 |
6.01e-04 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 39.29 E-value: 6.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 4 ANSVVVLDFETT---------GLSPNLgdraIEIGAVKLVNGEVVETFQQLMNPGF--RVSSFIESYTGITNNMLrsaps 72
Cdd:PRK07748 3 EQQFLFLDFEFTmpqhkkkpkGFFPEI----IEVGLVSVVGCEVEDTFSSYVKPKTfpSLTERCKSFLGITQEDV----- 73
|
90
....*....|..
gi 1219744296 73 cDEVMaSFSEFI 84
Cdd:PRK07748 74 -DKGI-SFEELV 83
|
|
| RNase_H_2 |
pfam13482 |
RNase_H superfamily; |
10-110 |
1.39e-03 |
|
RNase_H superfamily;
Pssm-ID: 433246 [Multi-domain] Cd Length: 163 Bit Score: 37.96 E-value: 1.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1219744296 10 LDFETTGLSPNLGDrAIEIGaVKLVNGEVVETFQQLMNPGFRVSSFIEsytgitnnmlrsapscdevmASFSEFIAGENL 89
Cdd:pfam13482 3 FDIETTGLSPGKNT-IYLIG-VYDVDGDKVRTFVQYLAEGPTEEAAIL--------------------QLFELLADYPLL 60
|
90 100
....*....|....*....|..
gi 1219744296 90 IAHN-ASFDKRFLDAELERIHC 110
Cdd:pfam13482 61 VTFNgKSFDVPFIKRRFKRYDL 82
|
|
| dexA |
PHA02570 |
exonuclease; Provisional |
8-62 |
3.80e-03 |
|
exonuclease; Provisional
Pssm-ID: 177399 Cd Length: 220 Bit Score: 36.97 E-value: 3.80e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1219744296 8 VVLDFETTGLSPNlgDRAIEIGAVKLV-NGEVVETFQQLMNPGFRVSSFIESYTGI 62
Cdd:PHA02570 4 FIIDFETFGNTPD--GAVIDLAVIAFEhDPHNPPTFEELVSRGRRIKFDLKSQKGK 57
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
31-92 |
4.29e-03 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins 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. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.
Pssm-ID: 99847 Cd Length: 152 Bit Score: 36.34 E-value: 4.29e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1219744296 31 VKLVN--GEVVetFQQLMNPGFRVSSFIESYTGITNNMLRSAPSCDEVMASFSEFIAGENLIAH 92
Cdd:cd06144 22 VSIVNedGNVV--YDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGH 83
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
3-48 |
6.78e-03 |
|
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: 36.62 E-value: 6.78e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1219744296 3 QANSVVVLDFETTGLSPNLgDRAIEIGAVKL-VNGEVVETFQQLMNP 48
Cdd:pfam13361 184 EQDNIVVFDVETTGLDTTE-DEIIQIAAIKLnKKGVVIESFERFLRL 229
|
|
| |
