|
Name |
Accession |
Description |
Interval |
E-value |
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
1-233 |
4.96e-143 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 399.30 E-value: 4.96e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 1 MFDSAIYWPARFAHLAQQARQPSLQRFYAQPLIEGSTPIHQCSLVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQAR 80
Cdd:PRK09146 6 MSQPALDWPAKFAQKAEQAKDPRLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQAR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 81 YWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHGKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLE 160
Cdd:PRK09146 86 HWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTME 165
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446382526 161 IERQLLDKQ-RSLWQRITRRPLPSIRLGQSRMRYHLPPYSPHHALTDAIATAELFQAQCAHHLPPHTAIQSLWL 233
Cdd:PRK09146 166 IEARIQRKQaGGLWNRLKGKKPESIRLADSRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSPDTPISKLWL 239
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
44-219 |
8.03e-48 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 154.95 E-value: 8.03e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 44 LVALDFETTGLNAEQDAIVSIGLVPFTTQRIFlsQARYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALH 123
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIV--ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 124 GKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLEIERQLLdkqrslwqritrRPLPSIRLGQSRMRYHLPPYSPHHA 203
Cdd:COG0847 80 GAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLL------------PGLPSYSLDALCERLGIPFDERHRA 147
|
170
....*....|....*.
gi 446382526 204 LTDAIATAELFQAQCA 219
Cdd:COG0847 148 LADAEATAELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
45-215 |
2.34e-41 |
|
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: 138.59 E-value: 2.34e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTtQRIFLSQARYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVD-GGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLEIERQLLdkqrslwqritrRPLPSIRLGQSRM-RYHLPPYSPHHA 203
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLL------------PGLRSHRLGLLLAeRYGIPLEGAHRA 147
|
170
....*....|..
gi 446382526 204 LTDAIATAELFQ 215
Cdd:cd06127 148 LADALATAELLL 159
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
43-222 |
1.81e-25 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 97.76 E-value: 1.81e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 43 SLVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARYwlVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEAL 122
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTY--VKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 123 HGKIVVVH------FRHIEREFLRQISLNIWgeaiEFPVLDTLEIErqlldkqrslwqRITRRPLPSIRLGQSRMRYHLP 196
Cdd:smart00479 79 RGRILVAGnsahfdLRFLKLEHPRLGIKQPP----KLPVIDTLKLA------------RATNPGLPKYSLKKLAKRLLLE 142
|
170 180
....*....|....*....|....*..
gi 446382526 197 PYSPHH-ALTDAIATAELFQAQCAHHL 222
Cdd:smart00479 143 VIQRAHrALDDARATAKLFKKLLERLE 169
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
45-214 |
4.28e-12 |
|
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: 61.98 E-value: 4.28e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARYWLVKPSQP--LEEESIVFHGITHSELQHAQAPEQVLKELLEAL 122
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 123 -HGKIVVVHFRHIEREFLRQI-SLNIWGEAIEF-PVLDTLEIERQLldkqrslwqrITRRPLPSIrlgqSRMRYHLPP-- 197
Cdd:pfam00929 81 rKGNLLVAHNASFDVGFLRYDdKRFLKKPMPKLnPVIDTLILDKAT----------YKELPGRSL----DALAEKLGLeh 146
|
170
....*....|....*...
gi 446382526 198 -YSPHHALTDAIATAELF 214
Cdd:pfam00929 147 iGRAHRALDDARATAKLF 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
45-229 |
5.45e-12 |
|
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: 62.85 E-value: 5.45e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDaIVSIGLVPFTTQRIFLSQARYWLvKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:TIGR00573 10 TTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYI-KPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVHFRHIEREFL-RQISLNIWGEAIEFPVLDTLEIERQLLDKqrslwqritrRPLPSIRLGQSRMRYHLPPYSP--H 201
Cdd:TIGR00573 88 AELVIHNASFDVGFLnYEFSKLYKVEPKTNDVIDTTDTLQYARPE----------FPGKRNTLDALCKRYEITNSHRalH 157
|
170 180
....*....|....*....|....*...
gi 446382526 202 HALTDAIATAELFQAQCAHHLPPHTAIQ 229
Cdd:TIGR00573 158 GALADAFILAKLYLVMTGKQTKYGENEG 185
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK09146 |
PRK09146 |
DNA polymerase III subunit epsilon; Validated |
1-233 |
4.96e-143 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236392 [Multi-domain] Cd Length: 239 Bit Score: 399.30 E-value: 4.96e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 1 MFDSAIYWPARFAHLAQQARQPSLQRFYAQPLIEGSTPIHQCSLVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQAR 80
Cdd:PRK09146 6 MSQPALDWPAKFAQKAEQAKDPRLKRFYAAGLVSPDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVPFTLQRIRCRQAR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 81 YWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHGKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLE 160
Cdd:PRK09146 86 HWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTME 165
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446382526 161 IERQLLDKQ-RSLWQRITRRPLPSIRLGQSRMRYHLPPYSPHHALTDAIATAELFQAQCAHHLPPHTAIQSLWL 233
Cdd:PRK09146 166 IEARIQRKQaGGLWNRLKGKKPESIRLADSRLRYGLPAYSPHHALTDAIATAELLQAQIAHHFSPDTPISKLWL 239
|
|
| DnaQ |
COG0847 |
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ... |
44-219 |
8.03e-48 |
|
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];
Pssm-ID: 440608 [Multi-domain] Cd Length: 163 Bit Score: 154.95 E-value: 8.03e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 44 LVALDFETTGLNAEQDAIVSIGLVPFTTQRIFlsQARYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALH 123
Cdd:COG0847 2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRIV--ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 124 GKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLEIERQLLdkqrslwqritrRPLPSIRLGQSRMRYHLPPYSPHHA 203
Cdd:COG0847 80 GAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLL------------PGLPSYSLDALCERLGIPFDERHRA 147
|
170
....*....|....*.
gi 446382526 204 LTDAIATAELFQAQCA 219
Cdd:COG0847 148 LADAEATAELFLALLR 163
|
|
| DEDDh |
cd06127 |
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ... |
45-215 |
2.34e-41 |
|
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: 138.59 E-value: 2.34e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTtQRIFLSQARYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:cd06127 1 VVFDTETTGLDPKKDRIIEIGAVKVD-GGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLEIERQLLdkqrslwqritrRPLPSIRLGQSRM-RYHLPPYSPHHA 203
Cdd:cd06127 80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLL------------PGLRSHRLGLLLAeRYGIPLEGAHRA 147
|
170
....*....|..
gi 446382526 204 LTDAIATAELFQ 215
Cdd:cd06127 148 LADALATAELLL 159
|
|
| PolC |
COG2176 |
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ... |
45-216 |
5.97e-34 |
|
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];
Pssm-ID: 441779 [Multi-domain] Cd Length: 181 Bit Score: 119.86 E-value: 5.97e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRI---FlsqarYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEA 121
Cdd:COG2176 11 VVFDLETTGLSPKKDEIIEIGAVKVENGEIvdrF-----STLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 122 LHGKIVVVHFRHIEREFLRQiSLNIWGEAIEFPVLDTLEIERQLLDKqrslwqritrrpLPSIRLGQSRMRYHLPPYSPH 201
Cdd:COG2176 86 LGDAVLVAHNASFDLGFLNA-ALKRLGLPFDNPVLDTLELARRLLPE------------LKSYKLDTLAERLGIPLEDRH 152
|
170
....*....|....*
gi 446382526 202 HALTDAIATAELFQA 216
Cdd:COG2176 153 RALGDAEATAELFLK 167
|
|
| EXOIII |
smart00479 |
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ... |
43-222 |
1.81e-25 |
|
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;
Pssm-ID: 214685 [Multi-domain] Cd Length: 169 Bit Score: 97.76 E-value: 1.81e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 43 SLVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARYwlVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEAL 122
Cdd:smart00479 1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTY--VKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 123 HGKIVVVH------FRHIEREFLRQISLNIWgeaiEFPVLDTLEIErqlldkqrslwqRITRRPLPSIRLGQSRMRYHLP 196
Cdd:smart00479 79 RGRILVAGnsahfdLRFLKLEHPRLGIKQPP----KLPVIDTLKLA------------RATNPGLPKYSLKKLAKRLLLE 142
|
170 180
....*....|....*....|....*..
gi 446382526 197 PYSPHH-ALTDAIATAELFQAQCAHHL 222
Cdd:smart00479 143 VIQRAHrALDDARATAKLFKKLLERLE 169
|
|
| PRK09145 |
PRK09145 |
3'-5' exonuclease; |
8-214 |
5.67e-22 |
|
3'-5' exonuclease;
Pssm-ID: 236391 [Multi-domain] Cd Length: 202 Bit Score: 89.58 E-value: 5.67e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 8 WPARFAHLAQQARQ--PSLQRFYAQPliegstPIHQcsLVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARYWLVK 85
Cdd:PRK09145 1 MMNWLRRLWWRRRLkdPRYAFLFEPP------PPDE--WVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLELLVR 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 86 PSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHGKIVVVHFRHIEREFLRQISLNIWGeaIEFPVlDTLEIERQL 165
Cdd:PRK09145 73 PPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLG--IPLPN-PLIEVSALY 149
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 446382526 166 LDKqrslwqRITRRPLPSIRLGQSRMRYHL--PPYSPHHALTDAIATAELF 214
Cdd:PRK09145 150 YDK------KERHLPDAYIDLRFDAILKHLdlPVLGRHDALNDAIMAALIF 194
|
|
| PRK07740 |
PRK07740 |
hypothetical protein; Provisional |
15-216 |
5.95e-16 |
|
hypothetical protein; Provisional
Pssm-ID: 236085 [Multi-domain] Cd Length: 244 Bit Score: 74.32 E-value: 5.95e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 15 LAQQARQPSLQRfYAQPLIEGSTPIHQCSLVALDFETTGLNAEQ-DAIVSIGLVPFTTQRIFlSQARYWLVKPSQPLEEE 93
Cdd:PRK07740 33 LQQEAWIRSIQK-EAKRDDVLDIPLTDLPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVE-TDTFYSLVKPKRPIPEH 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 94 SIVFHGITHSELQHAQAPEQVLKELLEALHGKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTleierqlldkqrSLW 173
Cdd:PRK07740 111 ILELTGITAEDVAFAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDT------------MFL 178
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 446382526 174 QRITRRPLPSIRLGQSRMRYHLPPYSPHHALTDAIATAELFQA 216
Cdd:PRK07740 179 TKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTAKLWAI 221
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
45-214 |
3.34e-15 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 74.10 E-value: 3.34e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARywLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:PRK00448 422 VVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEF--FIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGD 499
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVH-----FRHIEREFLRqisLNIwgEAIEFPVLDTLEIERQLLDKQRSLwqritrrplpsiRLGQSRMRYHLPPYS 199
Cdd:PRK00448 500 SILVAHnasfdVGFINTNYEK---LGL--EKIKNPVIDTLELSRFLYPELKSH------------RLNTLAKKFGVELEH 562
|
170
....*....|....*
gi 446382526 200 PHHALTDAIATAELF 214
Cdd:PRK00448 563 HHRADYDAEATAYLL 577
|
|
| DNA_pol_III_epsilon_like |
cd06130 |
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ... |
45-214 |
3.88e-15 |
|
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: 70.23 E-value: 3.88e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTglNAEQDAIVSIGLVPFTTQRIflSQARYWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:cd06130 2 VAIDFETA--NADRASACSIGLVKVRDGQI--VDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVHFRHIEREFLRQiSLNIWG-EAIEFPVLDTLEIERQlldkqrsLWQRITRRPLPSIrlgqsrMRYHLPPYSPHHA 203
Cdd:cd06130 78 SLVVAHNASFDRSVLRA-ALEAYGlPPPPYQYLCTVRLARR-------VWPLLPNHKLNTV------AEHLGIELNHHDA 143
|
170
....*....|.
gi 446382526 204 LTDAIATAELF 214
Cdd:cd06130 144 LEDARACAEIL 154
|
|
| PRK07942 |
PRK07942 |
DNA polymerase III subunit epsilon; Provisional |
40-228 |
2.69e-12 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 181176 [Multi-domain] Cd Length: 232 Bit Score: 63.84 E-value: 2.69e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 40 HQCSLVALDFETTGLNAEQDAIVSIGLVPFTTQRIfLSQARYWLVKPSQPLEEESIVFHGITHSELQ-HAQAPEQVLKEL 118
Cdd:PRK07942 4 HPGPLAAFDLETTGVDPETARIVTAALVVVDADGE-VVESREWLADPGVEIPEEASAVHGITTEYARaHGRPAAEVLAEI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 119 LEALH-----GKIVVVHFRHIEREFLRQISLNIWGEAIE-FPVLDTLEIERQLlDKQRSlwqriTRRPLPSIRlgqsrMR 192
Cdd:PRK07942 83 ADALReawarGVPVVVFNAPYDLTVLDRELRRHGLPSLVpGPVIDPYVIDKAV-DRYRK-----GKRTLTALC-----EH 151
|
170 180 190
....*....|....*....|....*....|....*.
gi 446382526 193 YHLPPYSPHHALTDAIATAELFQAQCAHHlPPHTAI 228
Cdd:PRK07942 152 YGVRLDNAHEATADALAAARVAWALARRF-PELAAL 186
|
|
| RNase_T |
pfam00929 |
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ... |
45-214 |
4.28e-12 |
|
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: 61.98 E-value: 4.28e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQARYWLVKPSQP--LEEESIVFHGITHSELQHAQAPEQVLKELLEAL 122
Cdd:pfam00929 1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 123 -HGKIVVVHFRHIEREFLRQI-SLNIWGEAIEF-PVLDTLEIERQLldkqrslwqrITRRPLPSIrlgqSRMRYHLPP-- 197
Cdd:pfam00929 81 rKGNLLVAHNASFDVGFLRYDdKRFLKKPMPKLnPVIDTLILDKAT----------YKELPGRSL----DALAEKLGLeh 146
|
170
....*....|....*...
gi 446382526 198 -YSPHHALTDAIATAELF 214
Cdd:pfam00929 147 iGRAHRALDDARATAKLF 164
|
|
| dnaq |
TIGR00573 |
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ... |
45-229 |
5.45e-12 |
|
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: 62.85 E-value: 5.45e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDaIVSIGLVPFTTQRIFLSQARYWLvKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALHG 124
Cdd:TIGR00573 10 TTGDNETTGLYAGHD-IIEIGAVEIINRRITGNKFHTYI-KPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 125 KIVVVHFRHIEREFL-RQISLNIWGEAIEFPVLDTLEIERQLLDKqrslwqritrRPLPSIRLGQSRMRYHLPPYSP--H 201
Cdd:TIGR00573 88 AELVIHNASFDVGFLnYEFSKLYKVEPKTNDVIDTTDTLQYARPE----------FPGKRNTLDALCKRYEITNSHRalH 157
|
170 180
....*....|....*....|....*...
gi 446382526 202 HALTDAIATAELFQAQCAHHLPPHTAIQ 229
Cdd:TIGR00573 158 GALADAFILAKLYLVMTGKQTKYGENEG 185
|
|
| PRK07883 |
PRK07883 |
DEDD exonuclease domain-containing protein; |
37-222 |
8.18e-12 |
|
DEDD exonuclease domain-containing protein;
Pssm-ID: 236123 [Multi-domain] Cd Length: 557 Bit Score: 64.17 E-value: 8.18e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 37 TPIHQCSLVALDFETTGLNAEQDAIVSIGLVP---------FTTqriflsqarywLVKPSQPLEEESIVFHGITHSELQH 107
Cdd:PRK07883 10 TPLRDVTFVVVDLETTGGSPAGDAITEIGAVKvrggevlgeFAT-----------LVNPGRPIPPFITVLTGITTAMVAG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 108 AQAPEQVLKELLEALHGKIVVVHFRHIEREFLRQISLNIWGEAIEFPVLDTLEIERQLLdkqrslwqriTRRPLPSIRLG 187
Cdd:PRK07883 79 APPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVL----------PRDEAPNVRLS 148
|
170 180 190
....*....|....*....|....*....|....*.
gi 446382526 188 qSRMRYHLPPYSP-HHALTDAIATAELFqaqcaHHL 222
Cdd:PRK07883 149 -TLARLFGATTTPtHRALDDARATVDVL-----HGL 178
|
|
| PRK06807 |
PRK06807 |
3'-5' exonuclease; |
45-219 |
1.58e-10 |
|
3'-5' exonuclease;
Pssm-ID: 235864 [Multi-domain] Cd Length: 313 Bit Score: 59.83 E-value: 1.58e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRI---FLSqarywLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEA 121
Cdd:PRK06807 11 VVIDFETTGFNPYNDKIIQVAAVKYRNHELvdqFVS-----YVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 122 LHGKIVVVHFRHIEREFLRQiSLNIWG-EAIEFPVLDTLEIERQLLdkqrslwqritrRPLPSIRLGQSRmRYHLPPYSP 200
Cdd:PRK06807 86 LHTNVIVAHNASFDMRFLKS-NVNMLGlPEPKNKVIDTVFLAKKYM------------KHAPNHKLETLK-RMLGIRLSS 151
|
170
....*....|....*....
gi 446382526 201 HHALTDAIATAELFQaQCA 219
Cdd:PRK06807 152 HNAFDDCITCAAVYQ-KCA 169
|
|
| DNA_pol_III_epsilon_Ecoli_like |
cd06131 |
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ... |
44-170 |
3.09e-09 |
|
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: 54.46 E-value: 3.09e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 44 LVALDFETTGLNAEQ-DAIVSIGLVPFtTQRIFLSQARYWLVKPSQPLEEESIVFHGITHSELqhAQAP--EQVLKELLE 120
Cdd:cd06131 1 QIVLDTETTGLDPREgHRIIEIGCVEL-INRRLTGNTFHVYINPERDIPEEAFKVHGITDEFL--ADKPkfAEIADEFLD 77
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 446382526 121 ALHGKIVVVH-----FRHIEREFlrqiSLNIWGEAIEFP--VLDTLEIERQLLDKQR 170
Cdd:cd06131 78 FIRGAELVIHnasfdVGFLNAEL----SLLGLGKKIIDFcrVIDTLALARKKFPGKP 130
|
|
| PRK08074 |
PRK08074 |
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated |
45-216 |
9.78e-09 |
|
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236148 [Multi-domain] Cd Length: 928 Bit Score: 54.96 E-value: 9.78e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQ-DAIVSIGLVPFTTQRIFLSQARYwlVKPSQPL----EEesivFHGITHSELQHAQAPEQVLKELL 119
Cdd:PRK08074 6 VVVDLETTGNSPKKgDKIIQIAAVVVEDGEILERFSSF--VNPERPIppfiTE----LTGISEEMVKQAPLFEDVAPEIV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 120 EALHGKIVVVHFRHIEREFL-RQISLNIWGEaIEFPVLDTLEIERQLLDKQrslwqritrrplPSIRLGQSRMRYHLPPY 198
Cdd:PRK08074 80 ELLEGAYFVAHNVHFDLNFLnEELERAGYTE-IHCPKLDTVELARILLPTA------------ESYKLRDLSEELGLEHD 146
|
170
....*....|....*...
gi 446382526 199 SPHHALTDAIATAELFQA 216
Cdd:PRK08074 147 QPHRADSDAEVTAELFLQ 164
|
|
| PRK06310 |
PRK06310 |
DNA polymerase III subunit epsilon; Validated |
45-218 |
1.58e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180525 [Multi-domain] Cd Length: 250 Bit Score: 53.68 E-value: 1.58e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQAryWLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEAL-H 123
Cdd:PRK06310 10 VCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVE--FLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFkE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 124 GKIVVVHFRHIEREFLRQISLNIwGEAI---EFPVLDTLEIERQLLDKqrslwqritrrplPSIRLGQSRMRYHLPPYSP 200
Cdd:PRK06310 88 GDYIVGHSVGFDLQVLSQESERI-GETFlskHYYIIDTLRLAKEYGDS-------------PNNSLEALAVHFNVPYDGN 153
|
170
....*....|....*...
gi 446382526 201 HHALTDAIATAELFQAQC 218
Cdd:PRK06310 154 HRAMKDVEINIKVFKHLC 171
|
|
| PRK06309 |
PRK06309 |
DNA polymerase III subunit epsilon; Validated |
44-216 |
6.97e-08 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 180524 [Multi-domain] Cd Length: 232 Bit Score: 51.35 E-value: 6.97e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 44 LVALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSqarywLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEALH 123
Cdd:PRK06309 4 LIFYDTETTGTQIDKDRIIEIAAYNGVTSESFQT-----LVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 124 GK-IVVVH------FRHIEREFLRQislniwgeAIEFPVLDTLEierqlldkqrSL-WQRITRRPLPSIRLGQSRMRYHL 195
Cdd:PRK06309 79 TDnILVAHnndafdFPLLRKECRRH--------GLEPPTLRTID----------SLkWAQKYRPDLPKHNLQYLRQVYGF 140
|
170 180
....*....|....*....|.
gi 446382526 196 PPYSPHHALTDAIATAELFQA 216
Cdd:PRK06309 141 EENQAHRALDDVITLHRVFSA 161
|
|
| PRK06063 |
PRK06063 |
DEDDh family exonuclease; |
48-216 |
6.15e-06 |
|
DEDDh family exonuclease;
Pssm-ID: 180377 [Multi-domain] Cd Length: 313 Bit Score: 46.23 E-value: 6.15e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 48 DFETTGLNAEQDAIVSIGLVPfTTQRIFLSQARYWLVKPSqpLEEESIVFHGITHSELQHAQAPEQVLKELLEALHGKIV 127
Cdd:PRK06063 21 DVETSGFRPGQARIISLAVLG-LDADGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGRTL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 128 VVH-----FRHIEREFLRQislniwgeAIEFPV---LDTLEIERQLldkqrslwqritRRPLPSIRLGQSRMRYHLPPYS 199
Cdd:PRK06063 98 VAHnvafdYSFLAAEAERA--------GAELPVdqvMCTVELARRL------------GLGLPNLRLETLAAHWGVPQQR 157
|
170
....*....|....*..
gi 446382526 200 PHHALTDAIATAELFQA 216
Cdd:PRK06063 158 PHDALDDARVLAGILRP 174
|
|
| PRK09182 |
PRK09182 |
DNA polymerase III subunit epsilon; Validated |
45-139 |
8.34e-06 |
|
DNA polymerase III subunit epsilon; Validated
Pssm-ID: 236397 [Multi-domain] Cd Length: 294 Bit Score: 45.74 E-value: 8.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFT---TQRIFLSQARY-WLVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLE 120
Cdd:PRK09182 40 VILDTETTGLDPRKDEIIEIGMVAFEyddDGRIGDVLDTFgGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAAVDALIA 119
|
90
....*....|....*....
gi 446382526 121 alHGKIVVVHFRHIEREFL 139
Cdd:PRK09182 120 --PADLIIAHNAGFDRPFL 136
|
|
| Rv2179c-like |
pfam16473 |
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ... |
45-216 |
2.51e-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: 40.49 E-value: 2.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFETTGlNAEQDAIVSIGLVPFTTQRIFLSQARYWLVKPsQPLEEES--IVFHGITHSELQHAQAPEQVLKEllEAL 122
Cdd:pfam16473 3 LMIDIETLG-NEPTAPIVSIGAVFFDPETGELGKEFYARIDL-ESSMSAGatIDADTILWWLKQSSEARAQLLGD--DAP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 123 HGKIVVVHFRHIEREFLRQISLNIWGEAIEF--PVLdtleieRQLLDKQRS--LWQRITRRPLPSIRLGQSRMRYHLPPY 198
Cdd:pfam16473 79 SLPDALLDLNDFIRDNGDPKSLKVWGNGASFdnVIL------RAAFERGGLpaPWKYWNDRDVRTIVALGPELGYDPKRD 152
|
170 180
....*....|....*....|...
gi 446382526 199 SP-----HHALTDAIATAELFQA 216
Cdd:pfam16473 153 IPfegvkHNALDDAIHQAKYVSA 175
|
|
| PRK05711 |
PRK05711 |
DNA polymerase III subunit epsilon; Provisional |
47-172 |
1.10e-03 |
|
DNA polymerase III subunit epsilon; Provisional
Pssm-ID: 235574 [Multi-domain] Cd Length: 240 Bit Score: 39.07 E-value: 1.10e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 47 LDFETTGLNAEQ-DAIVSIGLVP----FTTQRIFlsqARYwlVKPSQPLEEESIVFHGITHSELqhAQAPE--QVLKELL 119
Cdd:PRK05711 9 LDTETTGLNQREgHRIIEIGAVElinrRLTGRNF---HVY--IKPDRLVDPEALAVHGITDEFL--ADKPTfaEVADEFL 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446382526 120 EALHGKIVVVH-------FrhIEREFlRQISLNIwGEAIEFP-VLDTLEIERQLLDKQR-SL 172
Cdd:PRK05711 82 DFIRGAELIIHnapfdigF--MDYEF-ALLGRDI-PKTNTFCkVTDTLAMARRMFPGKRnSL 139
|
|
| DEDDh_RNase |
cd06137 |
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ... |
45-108 |
5.50e-03 |
|
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.
Pssm-ID: 99840 Cd Length: 161 Bit Score: 36.49 E-value: 5.50e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446382526 45 VALDFETTGLNAEQDAIVSIGLVPFTTQRIFLSQarywLVKPSQPLEEESIVFHGITHSELQHA 108
Cdd:cd06137 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDS----LVRPSVRVTDWRTRFSGVTPADLEEA 60
|
|
| REX4_like |
cd06144 |
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ... |
45-130 |
8.96e-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: 35.57 E-value: 8.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446382526 45 VALDFE--TTGLNAEQDAIVSIGLVPFTTQRIFLSqarYwlVKPSQPLEEESIVFHGITHSELQHAQAPEQVLKELLEAL 122
Cdd:cd06144 1 VALDCEmvGVGPDGSESALARVSIVNEDGNVVYDT---Y--VKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELL 75
|
....*...
gi 446382526 123 HGKIVVVH 130
Cdd:cd06144 76 KGRILVGH 83
|
|
| |
