|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
1-281 |
0e+00 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 575.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 1 MKNATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEIGTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQI 80
Cdd:PRK06722 1 MENATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 81 IEKFIQFIGEGSIFVSWGKEDYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEELFEHTPSLQFAVEQLALTWEGKQ 160
Cdd:PRK06722 81 IEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 161 HRALADAENTANILLKVYSERDINKRYKRHGELELVKNGKLTEKAKKKMRKWVFKELKKNTERPFEWSTFESGDTWESIT 240
Cdd:PRK06722 161 HRALADAENTANILLKAYSERDITKRYKRHGELELVKNGKLTEKAKKKMRKWVFKEMRKNTERPFVWSTFESSDTWESIT 240
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 446709071 241 ERYYISENTVELLKKHFRTAVRKAERQIRYLAEMEENTEVK 281
Cdd:PRK06722 241 ERYYISESTIELLKKHFRTAVRKAERQIRYLAEMEKVVEEN 281
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
7-178 |
2.65e-46 |
|
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: 153.14 E-value: 2.65e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERN--FRPYKSEDPSEIVDIGAVKIEIGTMKIIEEFSELVKPSA--RLTRHTTKLTGITKKDLMGVEKFPQIIE 82
Cdd:cd06133 1 YLVIDFEATcwEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 83 KFIQFIGEGS--IFVSWGKEDYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEelFEHTPSLQFAVEQLALTWEGKQ 160
Cdd:cd06133 81 EFLEWLGKNGkyAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG--LKKRTGLSKALEYLGLEFEGRH 158
|
170
....*....|....*...
gi 446709071 161 HRALADAENTANILLKVY 178
Cdd:cd06133 159 HRGLDDARNIARILKRLL 176
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
6-183 |
1.05e-43 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 146.93 E-value: 1.05e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 6 HFIVFDIERN--FRPYKSEDPSEIVDIGAVKIEIGTmKIIEEFSELVKPSAR--LTRHTTKLTGITKKDLMGVEKFPQII 81
Cdd:COG5018 3 KYLVIDLEATcwDGKPPPGFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRpkLSPFCTELTGITQEDVDSAPSFAEAI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 82 EKFIQFIG-EGSIFVSWGKEDYRFLSHDCTLYGVECPSIEKEnrIDLQKFvFQAYEELfEHTPSLQFAVEQLALTWEGKQ 160
Cdd:COG5018 82 EDFKKWIGsEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRH--INLKKL-FALYFGL-KKRIGLKKALELLGLEFEGTH 157
|
170 180
....*....|....*....|...
gi 446709071 161 HRALADAENTANILLKVYSERDI 183
Cdd:COG5018 158 HRALDDARNTAKLFKKILGDKRL 180
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
7-177 |
1.21e-23 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 94.29 E-value: 1.21e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERNfrpYKSEDPSEIVDIGAVKIEigTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:smart00479 2 LVVIDCETT---GLDPGKDEIIEIAAVDVD--GGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGEGSIFV-SWGKEDYRFLSHDCTLYGVECPsiEKENRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGKQHRALA 165
Cdd:smart00479 77 FLRGRILVAgNSAHFDLRFLKLEHPRLGIKQP--PKLPVIDTLKLARATNPGLPKY--SLKKLAKRLLLEVIQRAHRALD 152
|
170
....*....|..
gi 446709071 166 DAENTANILLKV 177
Cdd:smart00479 153 DARATAKLFKKL 164
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
8-174 |
7.50e-20 |
|
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: 83.94 E-value: 7.50e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 8 IVFDIERN-FRPYKSEdpseIVDIGAVKIEIGTMKIIEEFSELVKP--SARLTRHTTKLTGITKKDLMGVEKFPQIIEKF 84
Cdd:pfam00929 1 VVIDLETTgLDPEKDE----IIEIAAVVIDGGENEIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 85 IQFIGEGSIFVSWGKE-DYRFLSHDCTLYG-VECPSIEKenRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGKQHR 162
Cdd:pfam00929 77 LEFLRKGNLLVAHNASfDVGFLRYDDKRFLkKPMPKLNP--VIDTLILDKATYKELPGR--SLDALAEKLGLEHIGRAHR 152
|
170
....*....|..
gi 446709071 163 ALADAENTANIL 174
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
7-178 |
2.99e-08 |
|
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: 52.84 E-value: 2.99e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERNfRPYKSEDpseIVDIGAVKIeIGTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:TIGR00573 9 ETTGDNETT-GLYAGHD---IIEIGAVEI-INRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGeGSIFVSWGKE-DYRFLSHDCT-LYGVECPSIEKENRIDLQKFVFQAYeelfehtPSLQFAVEQLALTWEGKQH-RA 163
Cdd:TIGR00573 84 YIR-GAELVIHNASfDVGFLNYEFSkLYKVEPKTNDVIDTTDTLQYARPEF-------PGKRNTLDALCKRYEITNShRA 155
|
170
....*....|....*
gi 446709071 164 LADAENTANILLKVY 178
Cdd:TIGR00573 156 LHGALADAFILAKLY 170
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06722 |
PRK06722 |
exonuclease; Provisional |
1-281 |
0e+00 |
|
exonuclease; Provisional
Pssm-ID: 180670 [Multi-domain] Cd Length: 281 Bit Score: 575.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 1 MKNATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEIGTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQI 80
Cdd:PRK06722 1 MENATHFIVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 81 IEKFIQFIGEGSIFVSWGKEDYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEELFEHTPSLQFAVEQLALTWEGKQ 160
Cdd:PRK06722 81 IEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 161 HRALADAENTANILLKVYSERDINKRYKRHGELELVKNGKLTEKAKKKMRKWVFKELKKNTERPFEWSTFESGDTWESIT 240
Cdd:PRK06722 161 HRALADAENTANILLKAYSERDITKRYKRHGELELVKNGKLTEKAKKKMRKWVFKEMRKNTERPFVWSTFESSDTWESIT 240
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 446709071 241 ERYYISENTVELLKKHFRTAVRKAERQIRYLAEMEENTEVK 281
Cdd:PRK06722 241 ERYYISESTIELLKKHFRTAVRKAERQIRYLAEMEKVVEEN 281
|
|
| ERI-1_3'hExo_like |
cd06133 |
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ... |
7-178 |
2.65e-46 |
|
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: 153.14 E-value: 2.65e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERN--FRPYKSEDPSEIVDIGAVKIEIGTMKIIEEFSELVKPSA--RLTRHTTKLTGITKKDLMGVEKFPQIIE 82
Cdd:cd06133 1 YLVIDFEATcwEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 83 KFIQFIGEGS--IFVSWGKEDYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEelFEHTPSLQFAVEQLALTWEGKQ 160
Cdd:cd06133 81 EFLEWLGKNGkyAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG--LKKRTGLSKALEYLGLEFEGRH 158
|
170
....*....|....*...
gi 446709071 161 HRALADAENTANILLKVY 178
Cdd:cd06133 159 HRGLDDARNIARILKRLL 176
|
|
| KapD |
COG5018 |
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ... |
6-183 |
1.05e-43 |
|
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];
Pssm-ID: 444042 [Multi-domain] Cd Length: 181 Bit Score: 146.93 E-value: 1.05e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 6 HFIVFDIERN--FRPYKSEDPSEIVDIGAVKIEIGTmKIIEEFSELVKPSAR--LTRHTTKLTGITKKDLMGVEKFPQII 81
Cdd:COG5018 3 KYLVIDLEATcwDGKPPPGFPMEIIEIGAVKVDENG-EIIDEFSSFVKPVRRpkLSPFCTELTGITQEDVDSAPSFAEAI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 82 EKFIQFIG-EGSIFVSWGKEDYRFLSHDCTLYGVECPSIEKEnrIDLQKFvFQAYEELfEHTPSLQFAVEQLALTWEGKQ 160
Cdd:COG5018 82 EDFKKWIGsEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRH--INLKKL-FALYFGL-KKRIGLKKALELLGLEFEGTH 157
|
170 180
....*....|....*....|...
gi 446709071 161 HRALADAENTANILLKVYSERDI 183
Cdd:COG5018 158 HRALDDARNTAKLFKKILGDKRL 180
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
2-180 |
1.30e-32 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 117.94 E-value: 1.30e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 2 KNATHFIVFDIERN-FRPYKSEdpseIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQI 80
Cdd:COG2176 5 LEDLTYVVFDLETTgLSPKKDE----IIEIGAVKVENG--EIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEV 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 81 IEKFIQFIGeGSIFVSWGKE-DYRFLSHDCTLYGVECpsieKENRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEgK 159
Cdd:COG2176 79 LPEFLEFLG-DAVLVAHNASfDLGFLNAALKRLGLPF----DNPVLDTLELARRLLPELKSY--KLDTLAERLGIPLE-D 150
|
170 180
....*....|....*....|.
gi 446709071 160 QHRALADAENTANILLKVYSE 180
Cdd:COG2176 151 RHRALGDAEATAELFLKLLEK 171
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
7-176 |
4.10e-25 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 97.94 E-value: 4.10e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIER-NFRPYKSEdpseIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFI 85
Cdd:COG0847 2 FVVLDTETtGLDPAKDR----IIEIGAVKVDDG--RIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 86 QFIgEGSIFVSWGKE-DYRFLSHDCTLYGVECPSIEKenrIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGkQHRAL 164
Cdd:COG0847 76 EFL-GGAVLVAHNAAfDLGFLNAELRRAGLPLPPFPV---LDTLRLARRLLPGLPSY--SLDALCERLGIPFDE-RHRAL 148
|
170
....*....|..
gi 446709071 165 ADAENTANILLK 176
Cdd:COG0847 149 ADAEATAELFLA 160
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
7-177 |
1.21e-23 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 94.29 E-value: 1.21e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERNfrpYKSEDPSEIVDIGAVKIEigTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:smart00479 2 LVVIDCETT---GLDPGKDEIIEIAAVDVD--GGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGEGSIFV-SWGKEDYRFLSHDCTLYGVECPsiEKENRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGKQHRALA 165
Cdd:smart00479 77 FLRGRILVAgNSAHFDLRFLKLEHPRLGIKQP--PKLPVIDTLKLARATNPGLPKY--SLKKLAKRLLLEVIQRAHRALD 152
|
170
....*....|..
gi 446709071 166 DAENTANILLKV 177
Cdd:smart00479 153 DARATAKLFKKL 164
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
8-175 |
2.34e-22 |
|
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: 90.44 E-value: 2.34e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 8 IVFDIERN-FRPYKSEdpseIVDIGAVKIEIGtMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:cd06127 1 VVFDTETTgLDPKKDR----IIEIGAVKVDGG-IEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGeGSIFVSWGKE-DYRFLSHDCTLYGVEcpsIEKENRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGKQHRALA 165
Cdd:cd06127 76 FLG-GRVLVAHNASfDLRFLNRELRRLGGP---PLPNPWIDTLRLARRLLPGLRSH--RLGLLLAERYGIPLEGAHRALA 149
|
170
....*....|
gi 446709071 166 DAENTANILL 175
Cdd:cd06127 150 DALATAELLL 159
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
8-174 |
7.50e-20 |
|
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: 83.94 E-value: 7.50e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 8 IVFDIERN-FRPYKSEdpseIVDIGAVKIEIGTMKIIEEFSELVKP--SARLTRHTTKLTGITKKDLMGVEKFPQIIEKF 84
Cdd:pfam00929 1 VVIDLETTgLDPEKDE----IIEIAAVVIDGGENEIGETFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 85 IQFIGEGSIFVSWGKE-DYRFLSHDCTLYG-VECPSIEKenRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWEGKQHR 162
Cdd:pfam00929 77 LEFLRKGNLLVAHNASfDVGFLRYDDKRFLkKPMPKLNP--VIDTLILDKATYKELPGR--SLDALAEKLGLEHIGRAHR 152
|
170
....*....|..
gi 446709071 163 ALADAENTANIL 174
Cdd:pfam00929 153 ALDDARATAKLF 164
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
1-210 |
9.36e-19 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 86.05 E-value: 9.36e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 1 MKNAThFIVFDIE------RNfrpyksedpSEIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGV 74
Cdd:PRK00448 416 LKDAT-YVVFDVEttglsaVY---------DEIIEIGAVKIKNG--EIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDA 483
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 75 EKFPQIIEKFIQFIGeGSIFVSW-GKEDYRFLSHDCTLYG---VECPSIEKenrIDLQKFVfqaYEELFEHtpSLQFAVE 150
Cdd:PRK00448 484 PSIEEVLPKFKEFCG-DSILVAHnASFDVGFINTNYEKLGlekIKNPVIDT---LELSRFL---YPELKSH--RLNTLAK 554
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446709071 151 QLALTWEgKQHRALADAENTANILLKVYS---ERDINKrykrHGELELVKNGkltEKAKKKMR 210
Cdd:PRK00448 555 KFGVELE-HHHRADYDAEATAYLLIKFLKdlkEKGITN----LDELNKKLGS---EDAYKKAR 609
|
|
| PRK07748 |
PRK07748 |
3'-5' exonuclease KapD; |
14-205 |
2.42e-16 |
|
3'-5' exonuclease KapD;
Pssm-ID: 236087 Cd Length: 207 Bit Score: 75.49 E-value: 2.42e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 14 RNFRPyksedpsEIVDIGAVKIEIGTmkIIEEFSELVKPS--ARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQFIGEG 91
Cdd:PRK07748 23 KGFFP-------EIIEVGLVSVVGCE--VEDTFSSYVKPKtfPSLTERCKSFLGITQEDVDKGISFEELVEKLAEYDKRC 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 92 -SIFVSWGKEDYRFLSHDCTLYGVECPSIEKENRIDLQkfvfqaYEELF--EHTPSLQFAVEQLALTWEGKQHRALADAE 168
Cdd:PRK07748 94 kPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLE------YKKFFgeRNQTGLWKAIEEYGKEGTGKHHCALDDAM 167
|
170 180 190
....*....|....*....|....*....|....*..
gi 446709071 169 NTANILLKVYSERDINKRYKRHGELELVKNGKLTEKA 205
Cdd:PRK07748 168 TTYNIFKLVEKDKEYLVKPEPPTIGERVDFSKVLKKV 204
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
3-176 |
5.33e-13 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 68.83 E-value: 5.33e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 3 NATHFIVFDIERNFRPYKSEDpsEIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIE 82
Cdd:PRK08074 1 MSKRFVVVDLETTGNSPKKGD--KIIQIAAVVVEDG--EILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 83 KFIQFIgEGSIFVSWGKE-DYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEELfehtpSLQFAVEQLALTWEgKQH 161
Cdd:PRK08074 77 EIVELL-EGAYFVAHNVHfDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESY-----KLRDLSEELGLEHD-QPH 149
|
170
....*....|....*
gi 446709071 162 RALADAENTANILLK 176
Cdd:PRK08074 150 RADSDAEVTAELFLQ 164
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
7-175 |
1.42e-12 |
|
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: 64.07 E-value: 1.42e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERnfrpyKSEDPSEIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:cd06130 1 FVAIDFET-----ANADRASACSIGLVKVRDG--QIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGeGSIFVSWGKE-DYRFLSHDCTLYGVECPSIekeNRIDLQKFVFQAYEELFEHtpSLQFAVEQLALTWegKQHRALA 165
Cdd:cd06130 74 FLG-GSLVVAHNASfDRSVLRAALEAYGLPPPPY---QYLCTVRLARRVWPLLPNH--KLNTVAEHLGIEL--NHHDALE 145
|
170
....*....|
gi 446709071 166 DAENTANILL 175
Cdd:cd06130 146 DARACAEILL 155
|
|
| PRK07247 |
PRK07247 |
3'-5' exonuclease; |
1-198 |
1.14e-10 |
|
3'-5' exonuclease;
Pssm-ID: 180906 [Multi-domain] Cd Length: 195 Bit Score: 59.41 E-value: 1.14e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 1 MKNATHFIVFDIERNfrpyKSEDPSEIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQI 80
Cdd:PRK07247 1 MKRLETYIAFDLEFN----TVNGVSHIIQVSAVKYDDH--KEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 81 IEKFIQFIGEGSIFvswgkeDYRFLSHDCtlygvecpSIEKENRIDL-QKFVFQAYEELFEHTPSLQFAVEQLALT---- 155
Cdd:PRK07247 75 LAAFKEFVGELPLI------GYNAQKSDL--------PILAENGLDLsDQYQVDLYDEAFERRSSDLNGIANLKLQtvad 140
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 446709071 156 ---WEGKQHRALADAENTANILLKvYSERDINKRYKRHGELELVKN 198
Cdd:PRK07247 141 flgIKGRGHNSLEDARMTARVYES-FLESDQNKEYLEQQEEVTSDN 185
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
7-183 |
6.40e-10 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 58.14 E-value: 6.40e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERN-FRPYKSEdpsEIVDIGAVKIeIGTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFI 85
Cdd:PRK07740 61 FVVFDLETTgFSPQQGD---EILSIGAVKT-KGGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFY 136
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 86 QFIGEGSIFVSWGKEDYRFLSHdctlygvecpSIEKENR-------IDLQKFVFQAYEElfEHTPSLQFAVEQLALTWEG 158
Cdd:PRK07740 137 AFIGAGVLVAHHAGHDKAFLRH----------ALWRTYRqpfthrlIDTMFLTKLLAHE--RDFPTLDDALAYYGIPIPR 204
|
170 180
....*....|....*....|....*...
gi 446709071 159 KqHRALADAENTAN---ILLKVYSERDI 183
Cdd:PRK07740 205 R-HHALGDALMTAKlwaILLVEAQQRGI 231
|
|
| PRK08517 |
PRK08517 |
3'-5' exonuclease; |
7-174 |
1.15e-09 |
|
3'-5' exonuclease;
Pssm-ID: 236281 [Multi-domain] Cd Length: 257 Bit Score: 57.72 E-value: 1.15e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERN-FRPYKSEdpseIVDIGAVKIEIGtmKIIEEFSELVKpSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFI 85
Cdd:PRK08517 70 FCFVDIETNgSKPKKHQ----IIEIGAVKVKNG--EIIDRFESFVK-AKEVPEYITELTGITYEDLENAPSLKEVLEEFR 142
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 86 QFIGEgSIFVSWG-KEDYRFLSHDCTLYGVECPSIEKENRIDLQKFVFQAYEElfehtpSLQFAVEQLALTWEgKQHRAL 164
Cdd:PRK08517 143 LFLGD-SVFVAHNvNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRY------GLSFLKELLGIEIE-VHHRAY 214
|
170
....*....|
gi 446709071 165 ADAENTANIL 174
Cdd:PRK08517 215 ADALAAYEIF 224
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
7-178 |
2.99e-08 |
|
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: 52.84 E-value: 2.99e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERNfRPYKSEDpseIVDIGAVKIeIGTMKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQ 86
Cdd:TIGR00573 9 ETTGDNETT-GLYAGHD---IIEIGAVEI-INRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFAD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 87 FIGeGSIFVSWGKE-DYRFLSHDCT-LYGVECPSIEKENRIDLQKFVFQAYeelfehtPSLQFAVEQLALTWEGKQH-RA 163
Cdd:TIGR00573 84 YIR-GAELVIHNASfDVGFLNYEFSkLYKVEPKTNDVIDTTDTLQYARPEF-------PGKRNTLDALCKRYEITNShRA 155
|
170
....*....|....*
gi 446709071 164 LADAENTANILLKVY 178
Cdd:TIGR00573 156 LHGALADAFILAKLY 170
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
44-166 |
3.74e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 52.89 E-value: 3.74e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 44 EEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQFIGEGSIFVSWGKE--DYRFLSHDCTLYGVECPSIEK 121
Cdd:PRK06309 33 ESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNILVAHNNDafDFPLLRKECRRHGLEPPTLRT 112
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 446709071 122 enrIDLQKFVFQAYEELFEHtpSLQFAVEQLALTwEGKQHRALAD 166
Cdd:PRK06309 113 ---IDSLKWAQKYRPDLPKH--NLQYLRQVYGFE-ENQAHRALDD 151
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
7-203 |
5.98e-07 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 49.81 E-value: 5.98e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERN-FRPYKSEdpseIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFI 85
Cdd:PRK06807 10 YVVIDFETTgFNPYNDK----IIQVAAVKYRNH--ELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 86 QFIGEGSIFVSWGKEDYRFLSHDCTLYGVECPsieKENRIDlqkfVFQAYEELFEHTPSLQFAVEQLALTWEGKQHRALA 165
Cdd:PRK06807 84 AFLHTNVIVAHNASFDMRFLKSNVNMLGLPEP---KNKVID----TVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFD 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 446709071 166 DAENTANILLK-VYSERDINKRYKRHGELE----------LVKNGKLTE 203
Cdd:PRK06807 157 DCITCAAVYQKcASIEEEAKRKSNKEVLDEtavyeavkeiLVKNKRDIE 205
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
4-95 |
1.05e-06 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 49.53 E-value: 1.05e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 4 ATHFIVFDIERNfrpYKSEDPSEIVDIGAVKIEIGTmkIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEK 83
Cdd:PRK07883 14 DVTFVVVDLETT---GGSPAGDAITEIGAVKVRGGE--VLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88
|
90
....*....|..
gi 446709071 84 FIQFIGeGSIFV 95
Cdd:PRK07883 89 FLEFAR-GAVLV 99
|
|
| PRK07246 |
PRK07246 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
25-176 |
1.89e-06 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180905 [Multi-domain] Cd Length: 820 Bit Score: 48.91 E-value: 1.89e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 25 SEIVDIGAVKIEIGtmKIIEEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQFIgEGSIFVSWG-KEDYR 103
Cdd:PRK07246 23 ASIIQVGIVIIEGG--EIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLI-EDCIFVAHNvKFDAN 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446709071 104 FLSHDCTLYGVECpsieKENRID---LQKFVFQAYEELfehtpSLQFAVEQLALTWEgKQHRALADAENTANILLK 176
Cdd:PRK07246 100 LLAEALFLEGYEL----RTPRVDtveLAQVFFPTLEKY-----SLSHLSRELNIDLA-DAHTAIADARATAELFLK 165
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
23-177 |
8.64e-05 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 42.58 E-value: 8.64e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 23 DPS--EIVDIGAVKIEIGtmKII--EEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFIQFIGEGSIfVSWG 98
Cdd:PRK09145 42 DPRraEIVSIAAVKIRGN--RILtsERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPL-VGYY 118
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 99 KE-DYRFLSHDC-TLYGVECPsiekENRIDLQKFVfqaYEELFEHTP----SLQFA--VEQLAL-TWEgkQHRALADAEN 169
Cdd:PRK09145 119 LEfDVAMLNRYVrPLLGIPLP----NPLIEVSALY---YDKKERHLPdayiDLRFDaiLKHLDLpVLG--RHDALNDAIM 189
|
....*...
gi 446709071 170 TANILLKV 177
Cdd:PRK09145 190 AALIFLRL 197
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
8-126 |
9.06e-05 |
|
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: 42.13 E-value: 9.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 8 IVFDIERN-FRPYKSEdpsEIVDIGAVkiEIGTMKII-EEFSELVKPSARLTRHTTKLTGITKKDLMGVEKFPQIIEKFI 85
Cdd:cd06131 2 IVLDTETTgLDPREGH---RIIEIGCV--ELINRRLTgNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFL 76
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 446709071 86 QFIGEGSIFVSWGKEDYRFLSHDCTLYGVECPSIEKENRID 126
Cdd:cd06131 77 DFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID 117
|
|
| PTZ00315 |
PTZ00315 |
2'-phosphotransferase; Provisional |
7-90 |
1.36e-04 |
|
2'-phosphotransferase; Provisional
Pssm-ID: 240356 [Multi-domain] Cd Length: 582 Bit Score: 42.96 E-value: 1.36e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 7 FIVFDIERNF-RPYKSEDPsEIVDIGAVKIEIGTMKIIEEFSELVKP--SARLTRHTTKLTGITKKDLMGVEKFPQIIEK 83
Cdd:PTZ00315 58 YVVLDFEATCeADRRIEDA-EVIEFPMVLVDARTATPVAEFQRYVRPvkNPVLSRFCTELTGITQSMVSRADPFPVVYCE 136
|
....*..
gi 446709071 84 FIQFIGE 90
Cdd:PTZ00315 137 ALQFLAE 143
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
25-178 |
2.00e-03 |
|
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: 38.18 E-value: 2.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 25 SEIVDIGAVKIEIGTMKIIEEFSELVKPSARLTRHTT----------KLTGITKKDLMGVEK--FPQIIEKFIQFIGEGS 92
Cdd:pfam16473 16 APIVSIGAVFFDPETGELGKEFYARIDLESSMSAGATidadtilwwlKQSSEARAQLLGDDApsLPDALLDLNDFIRDNG 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446709071 93 IFVS---WGKE---DYRFLSHDCTLYGVECPSIEKENRiDLQKFVFQAYEELFEHTPSLQFaveqlaltwEGKQHRALAD 166
Cdd:pfam16473 96 DPKSlkvWGNGasfDNVILRAAFERGGLPAPWKYWNDR-DVRTIVALGPELGYDPKRDIPF---------EGVKHNALDD 165
|
170
....*....|..
gi 446709071 167 AENTANILLKVY 178
Cdd:pfam16473 166 AIHQAKYVSAIW 177
|
|
| REX1_like |
cd06145 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ... |
48-95 |
4.14e-03 |
|
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Pssm-ID: 99848 Cd Length: 150 Bit Score: 37.08 E-value: 4.14e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 446709071 48 ELVKPSARLTRHTTKLTGITKKDLMGVEK-FPQIIEKFIQFIGEGSIFV 95
Cdd:cd06145 32 ELVKPDGEIVDYNTRFSGITEEMLENVTTtLEDVQKKLLSLISPDTILV 80
|
|
| |
