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Conserved domains on  [gi|30690468|ref|NP_851083|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

3'-5' exonuclease( domain architecture ID 11270602)

3'-5' exonuclease similar to DNA polymerase III subunit epsilon and exodeoxyribonuclease 10

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 110-290 3.28e-44

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


:

Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 148.60  E-value: 3.28e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    110 TVIVSDLETTGLHRKNERIIEIAAQDIAGG-GYSTFQTLVNPGV-VPITNAHIHGIRNDMVCRPevPRMEELIPIFLRYV 187
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGeIIEVFDTYVKPDRpITDYATEIHGITPEMLDDA--PTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    188 ESRQkpggyvmLVAHNGKSFDFQFLINEFNRCSYEIPHNWLLLDSLPLARENMKSveptvKLSSSLEALADYYSLTREGD 267
Cdd:smart00479  79 RGRI-------LVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPG-----LPKYSLKKLAKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|...
gi 30690468    268 AHRALSDVLLLSKVFQKLTIDLK 290
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERLE 169
 
Name Accession Description Interval E-value
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 110-290 3.28e-44

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 148.60  E-value: 3.28e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    110 TVIVSDLETTGLHRKNERIIEIAAQDIAGG-GYSTFQTLVNPGV-VPITNAHIHGIRNDMVCRPevPRMEELIPIFLRYV 187
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGeIIEVFDTYVKPDRpITDYATEIHGITPEMLDDA--PTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    188 ESRQkpggyvmLVAHNGKSFDFQFLINEFNRCSYEIPHNWLLLDSLPLARENMKSveptvKLSSSLEALADYYSLTREGD 267
Cdd:smart00479  79 RGRI-------LVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPG-----LPKYSLKKLAKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|...
gi 30690468    268 AHRALSDVLLLSKVFQKLTIDLK 290
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERLE 169
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 109-285 1.01e-39

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 137.58  E-value: 1.01e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 109 LTVIVSDLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRY 186
Cdd:COG2176   8 LTYVVFDLETTGLSPKKDEIIEIGAVKVENGEiVDRFSTLVNPGRpIPPFITELTGITDEMV--ADAPPFEEVLPEFLEF 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 187 VesrqkpGGYVmLVAHNGkSFDFQFLINEFNRCSYEIPHNWllLDSLPLAREnmksVEPTVKlSSSLEALADYYSLTREg 266
Cdd:COG2176  86 L------GDAV-LVAHNA-SFDLGFLNAALKRLGLPFDNPV--LDTLELARR----LLPELK-SYKLDTLAERLGIPLE- 149

                       170
                ....*....|....*....
gi 30690468 267 DAHRALSDVLLLSKVFQKL 285
Cdd:COG2176 150 DRHRALGDAEATAELFLKL 168
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 112-283 3.96e-39

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: 135.12  E-value: 3.96e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 112 IVSDLETTGLHRKNERIIEIAAQDIAGGGY--STFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRYVE 188
Cdd:cd06127   1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEivERFETLVNPGRpIPPEATAIHGITDEML--ADAPPFEEVLPEFLEFLG 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 189 SRqkpggyvMLVAHNGkSFDFQFLINEFNRCSYEIPHNwLLLDSLPLAREnmksVEPTVKLSSSLEALADYYSLtREGDA 268
Cdd:cd06127  79 GR-------VLVAHNA-SFDLRFLNRELRRLGGPPLPN-PWIDTLRLARR----LLPGLRSHRLGLLLAERYGI-PLEGA 144

                       170
                ....*....|....*
gi 30690468 269 HRALSDVLLLSKVFQ 283
Cdd:cd06127 145 HRALADALATAELLL 159
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 110-301 7.11e-29

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 110.67  E-value: 7.11e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  110 TVIVSDLETTGLHRKNERIIEIAAQDIAGGgySTFQTLVNPGV-VPITNAHIHGIRNDMVCrpEVPRMEELipiflrYVE 188
Cdd:PRK06309   3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTS--ESFQTLVNPEIpIPAEASKIHGITTDEVA--DAPKFPEA------YQK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  189 SRQKPGGYVMLVAHNGKSFDFQFLINEFNRCSYEIPhNWLLLDSLPLAREnMKSVEPtvklSSSLEALADYYSLTrEGDA 268
Cdd:PRK06309  73 FIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPP-TLRTIDSLKWAQK-YRPDLP----KHNLQYLRQVYGFE-ENQA 145

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 30690468  269 HRALSDVLLLSKVFQKLTIDLKL--SLSDLVLRCH 301
Cdd:PRK06309 146 HRALDDVITLHRVFSALVGDLSPqqVYDLLNESCH 180
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 112-282 2.70e-21

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: 88.56  E-value: 2.70e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   112 IVSDLETTGLHRKNERIIEIAAQDIAGGGY---STFQTLVNPGV---VPITNAHIHGIRNDMVCrpEVPRMEELIPIFLR 185
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENeigETFHTYVKPTRlpkLTDECTKFTGITQAMLD--NKPSFEEVLEEFLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   186 YVESRQKpggyvmLVAHNgKSFDFQFLINEFNRCSY-EIPHNWLLLDSLPLARENMKSVEptvklSSSLEALADYYSLTR 264
Cdd:pfam00929  79 FLRKGNL------LVAHN-ASFDVGFLRYDDKRFLKkPMPKLNPVIDTLILDKATYKELP-----GRSLDALAEKLGLEH 146

                         170
                  ....*....|....*...
gi 30690468   265 EGDAHRALSDVLLLSKVF 282
Cdd:pfam00929 147 IGRAHRALDDARATAKLF 164
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 108-286 6.12e-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: 64.01  E-value: 6.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   108 LLTVIVSDLETTGlHRKNERIIEIAAQDIAGGGY--STFQTLVNPG-VVPITNAHIHGIRNDMVcrPEVPRMEELIPIFL 184
Cdd:TIGR00573   6 LDTETTGDNETTG-LYAGHDIIEIGAVEIINRRItgNKFHTYIKPDrPIDPDAIKIHGITDDML--KDKPDFKEIAEDFA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   185 RYVesrqkpGGYVmLVAHNGkSFDFQFLINEFNRCSYEIP--HNWLL-LDSLPLARENMKSVEPTvklsssLEALADYYS 261
Cdd:TIGR00573  83 DYI------RGAE-LVIHNA-SFDVGFLNYEFSKLYKVEPktNDVIDtTDTLQYARPEFPGKRNT------LDALCKRYE 148

                         170       180
                  ....*....|....*....|....*.
gi 30690468   262 LTREGDA-HRALSDVLLLSKVFQKLT 286
Cdd:TIGR00573 149 ITNSHRAlHGALADAFILAKLYLVMT 174
 
Name Accession Description Interval E-value
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 110-290 3.28e-44

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 148.60  E-value: 3.28e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    110 TVIVSDLETTGLHRKNERIIEIAAQDIAGG-GYSTFQTLVNPGV-VPITNAHIHGIRNDMVCRPevPRMEELIPIFLRYV 187
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGeIIEVFDTYVKPDRpITDYATEIHGITPEMLDDA--PTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    188 ESRQkpggyvmLVAHNGKSFDFQFLINEFNRCSYEIPHNWLLLDSLPLARENMKSveptvKLSSSLEALADYYSLTREGD 267
Cdd:smart00479  79 RGRI-------LVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPG-----LPKYSLKKLAKRLLLEVIQR 146

                          170       180
                   ....*....|....*....|...
gi 30690468    268 AHRALSDVLLLSKVFQKLTIDLK 290
Cdd:smart00479 147 AHRALDDARATAKLFKKLLERLE 169
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 109-285 1.01e-39

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 137.58  E-value: 1.01e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 109 LTVIVSDLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRY 186
Cdd:COG2176   8 LTYVVFDLETTGLSPKKDEIIEIGAVKVENGEiVDRFSTLVNPGRpIPPFITELTGITDEMV--ADAPPFEEVLPEFLEF 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 187 VesrqkpGGYVmLVAHNGkSFDFQFLINEFNRCSYEIPHNWllLDSLPLAREnmksVEPTVKlSSSLEALADYYSLTREg 266
Cdd:COG2176  86 L------GDAV-LVAHNA-SFDLGFLNAALKRLGLPFDNPV--LDTLELARR----LLPELK-SYKLDTLAERLGIPLE- 149

                       170
                ....*....|....*....
gi 30690468 267 DAHRALSDVLLLSKVFQKL 285
Cdd:COG2176 150 DRHRALGDAEATAELFLKL 168
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 112-283 3.96e-39

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: 135.12  E-value: 3.96e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 112 IVSDLETTGLHRKNERIIEIAAQDIAGGGY--STFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRYVE 188
Cdd:cd06127   1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEivERFETLVNPGRpIPPEATAIHGITDEML--ADAPPFEEVLPEFLEFLG 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 189 SRqkpggyvMLVAHNGkSFDFQFLINEFNRCSYEIPHNwLLLDSLPLAREnmksVEPTVKLSSSLEALADYYSLtREGDA 268
Cdd:cd06127  79 GR-------VLVAHNA-SFDLRFLNRELRRLGGPPLPN-PWIDTLRLARR----LLPGLRSHRLGLLLAERYGI-PLEGA 144

                       170
                ....*....|....*
gi 30690468 269 HRALSDVLLLSKVFQ 283
Cdd:cd06127 145 HRALADALATAELLL 159
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 111-286 1.31e-36

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 128.76  E-value: 1.31e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 111 VIVSDLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPGV-VPITNAHIHGIRNDMVCrpEVPRMEELIPIFLRYVE 188
Cdd:COG0847   2 FVVLDTETTGLDPAKDRIIEIGAVKVDDGRiVETFHTLVNPERpIPPEATAIHGITDEDVA--DAPPFAEVLPELLEFLG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 189 SRqkpggyvMLVAHNgKSFDFQFLINEFNRCSYEIPHNwLLLDSLPLARENMKSVEPTvklssSLEALADYYSLTREgDA 268
Cdd:COG0847  80 GA-------VLVAHN-AAFDLGFLNAELRRAGLPLPPF-PVLDTLRLARRLLPGLPSY-----SLDALCERLGIPFD-ER 144

                       170
                ....*....|....*...
gi 30690468 269 HRALSDVLLLSKVFQKLT 286
Cdd:COG0847 145 HRALADAEATAELFLALL 162
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 110-301 7.11e-29

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 110.67  E-value: 7.11e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  110 TVIVSDLETTGLHRKNERIIEIAAQDIAGGgySTFQTLVNPGV-VPITNAHIHGIRNDMVCrpEVPRMEELipiflrYVE 188
Cdd:PRK06309   3 ALIFYDTETTGTQIDKDRIIEIAAYNGVTS--ESFQTLVNPEIpIPAEASKIHGITTDEVA--DAPKFPEA------YQK 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  189 SRQKPGGYVMLVAHNGKSFDFQFLINEFNRCSYEIPhNWLLLDSLPLAREnMKSVEPtvklSSSLEALADYYSLTrEGDA 268
Cdd:PRK06309  73 FIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPP-TLRTIDSLKWAQK-YRPDLP----KHNLQYLRQVYGFE-ENQA 145

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 30690468  269 HRALSDVLLLSKVFQKLTIDLKL--SLSDLVLRCH 301
Cdd:PRK06309 146 HRALDDVITLHRVFSALVGDLSPqqVYDLLNESCH 180
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
110-274 1.23e-24

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 103.84  E-value: 1.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  110 TVIVSDLETTGLHRKNERIIEIAAQDIAGG---GysTFQTLVNPGV-VPITNAHIHGIRNDMVCrpEVPRMEELIPIFLR 185
Cdd:PRK07883  16 TFVVVDLETTGGSPAGDAITEIGAVKVRGGevlG--EFATLVNPGRpIPPFITVLTGITTAMVA--GAPPIEEVLPAFLE 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  186 YVesrqkpGGYVmLVAHNGkSFDFQFLINEFNRCSYEIPhNWLLLDSLPLARENMKSVE-PTVKLSssleALADYYSLTR 264
Cdd:PRK07883  92 FA------RGAV-LVAHNA-PFDIGFLRAAAARCGYPWP-GPPVLCTVRLARRVLPRDEaPNVRLS----TLARLFGATT 158

                        170
                 ....*....|
gi 30690468  265 EGDaHRALSD 274
Cdd:PRK07883 159 TPT-HRALDD 167
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 112-282 2.70e-21

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: 88.56  E-value: 2.70e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   112 IVSDLETTGLHRKNERIIEIAAQDIAGGGY---STFQTLVNPGV---VPITNAHIHGIRNDMVCrpEVPRMEELIPIFLR 185
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENeigETFHTYVKPTRlpkLTDECTKFTGITQAMLD--NKPSFEEVLEEFLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   186 YVESRQKpggyvmLVAHNgKSFDFQFLINEFNRCSY-EIPHNWLLLDSLPLARENMKSVEptvklSSSLEALADYYSLTR 264
Cdd:pfam00929  79 FLRKGNL------LVAHN-ASFDVGFLRYDDKRFLKkPMPKLNPVIDTLILDKATYKELP-----GRSLDALAEKLGLEH 146

                         170
                  ....*....|....*...
gi 30690468   265 EGDAHRALSDVLLLSKVF 282
Cdd:pfam00929 147 IGRAHRALDDARATAKLF 164
PRK06807 PRK06807
3'-5' exonuclease;
103-284 2.10e-20

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 89.49  E-value: 2.10e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  103 KDLSKLLTVIVSDLETTGLHRKNERIIEIAAQDIAGGGY-STFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELI 180
Cdd:PRK06807   2 GNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELvDQFVSYVNPERpIPDRITSLTGITNYRV--SDAPTIEEVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  181 PIFLRYVesRQKPggyvmLVAHNGkSFDFQFLINEFNRCSYEIPHNwLLLDSLPLARENMKSVEptvklSSSLEALADYy 260
Cdd:PRK06807  80 PLFLAFL--HTNV-----IVAHNA-SFDMRFLKSNVNMLGLPEPKN-KVIDTVFLAKKYMKHAP-----NHKLETLKRM- 144

                        170       180
                 ....*....|....*....|....
gi 30690468  261 sLTREGDAHRALSDVLLLSKVFQK 284
Cdd:PRK06807 145 -LGIRLSSHNAFDDCITCAAVYQK 167
polC PRK00448
DNA polymerase III PolC; Validated
 101-296 3.22e-20

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 91.44  E-value: 3.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   101 QDKDLSKLlTVIVSDLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPGvVPI----TNahIHGIRNDMVcrPEVPR 175
Cdd:PRK00448  412 VDRDLKDA-TYVVFDVETTGLSAVYDEIIEIGAVKIKNGEiIDKFEFFIKPG-HPLsaftTE--LTGITDDMV--KDAPS 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   176 MEELIPIFLRYVESRqkpggyvMLVAHNGkSFDFQFLINEFNRCSYEIPHNwLLLDSLPLARenmkSVEPTVKlSSSLEA 255
Cdd:PRK00448  486 IEEVLPKFKEFCGDS-------ILVAHNA-SFDVGFINTNYEKLGLEKIKN-PVIDTLELSR----FLYPELK-SHRLNT 551

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 30690468   256 LADYYSLTREgDAHRALSDVLLLSKVFQKLTIDLK----LSLSDL 296
Cdd:PRK00448  552 LAKKFGVELE-HHHRADYDAEATAYLLIKFLKDLKekgiTNLDEL 595
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 115-286 2.46e-19

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 85.27  E-value: 2.46e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  115 DLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPG-VVPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRYVESRQk 192
Cdd:PRK06310  13 DCETTGLDVKKDRIIEFAAIRFTFDEvIDSVEFLINPErVVSAESQRIHHISDAML--RDKPKIAEVFPQIKGFFKEGD- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  193 pggyvMLVAHnGKSFDFQFLINEFNRC--SYEIPHNWlLLDSLPLARENMKSvePTvklsSSLEALADYYSLTREGdAHR 270
Cdd:PRK06310  90 -----YIVGH-SVGFDLQVLSQESERIgeTFLSKHYY-IIDTLRLAKEYGDS--PN----NSLEALAVHFNVPYDG-NHR 155

                        170
                 ....*....|....*.
gi 30690468  271 ALSDVLLLSKVFQKLT 286
Cdd:PRK06310 156 AMKDVEINIKVFKHLC 171
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 112-286 5.82e-19

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: 82.19  E-value: 5.82e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 112 IVSDLETTGL-HRKNERIIEIAAQDIAGGGY--STFQTLVNPGV-VPITNAHIHGIRNDMVcrPEVPRMEELIPIFLRYV 187
Cdd:cd06131   2 IVLDTETTGLdPREGHRIIEIGCVELINRRLtgNTFHVYINPERdIPEEAFKVHGITDEFL--ADKPKFAEIADEFLDFI 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 188 ESRQkpggyvmLVAHNGkSFDFQFLINEFNRCSYEIP----HNWllLDSLPLARENMksvePTVKlsSSLEALADYYSLT 263
Cdd:cd06131  80 RGAE-------LVIHNA-SFDVGFLNAELSLLGLGKKiidfCRV--IDTLALARKKF----PGKP--NSLDALCKRFGID 143

                       170       180
                ....*....|....*....|....
gi 30690468 264 REG-DAHRALSDVLLLSKVFQKLT 286
Cdd:cd06131 144 NSHrTLHGALLDAELLAEVYLELT 167
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 112-285 2.04e-18

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 85.77  E-value: 2.04e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  112 IVSDLETTGlH--RKNERIIEIAAQDIAGGG-YSTFQTLVNPGV-VP--ITNahIHGIRNDMVcrPEVPRMEELIPIFLR 185
Cdd:PRK08074   6 VVVDLETTG-NspKKGDKIIQIAAVVVEDGEiLERFSSFVNPERpIPpfITE--LTGISEEMV--KQAPLFEDVAPEIVE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  186 YVEsrqkpGGYvmLVAHNgKSFDFQFLINEFNRCSYEIPHNwLLLDSLPLARenmkSVEPTVKlSSSLEALADYYSLTRE 265
Cdd:PRK08074  81 LLE-----GAY--FVAHN-VHFDLNFLNEELERAGYTEIHC-PKLDTVELAR----ILLPTAE-SYKLRDLSEELGLEHD 146

                        170       180
                 ....*....|....*....|
gi 30690468  266 gDAHRALSDVLLLSKVFQKL 285
Cdd:PRK08074 147 -QPHRADSDAEVTAELFLQL 165
PRK06063 PRK06063
DEDDh family exonuclease;
113-284 6.48e-16

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 76.66  E-value: 6.48e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  113 VSDLETTGLHRKNERIIEIAAQDIAGGGY--STFQTLVNPGVVPiTNAHIHGIRNDMV-CRPEVPRM-EELIPIfLRyve 188
Cdd:PRK06063  19 VVDVETSGFRPGQARIISLAVLGLDADGNveQSVVTLLNPGVDP-GPTHVHGLTAEMLeGQPQFADIaGEVAEL-LR--- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  189 srqkpgGYVmLVAHNGkSFDFQFLINEFNRCSYEIPHNWLLLdSLPLARE------NMKsveptvklsssLEALADYYSL 262
Cdd:PRK06063  94 ------GRT-LVAHNV-AFDYSFLAAEAERAGAELPVDQVMC-TVELARRlglglpNLR-----------LETLAAHWGV 153

                        170       180
                 ....*....|....*....|..
gi 30690468  263 TREgDAHRALSDVLLLSKVFQK 284
Cdd:PRK06063 154 PQQ-RPHDALDDARVLAGILRP 174
PRK07740 PRK07740
hypothetical protein; Provisional
 109-312 3.06e-15

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 73.93  E-value: 3.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  109 LTVIVSDLETTGLH-RKNERIIEIAAQDIAGG--GYSTFQTLVNPG-VVPITNAHIHGIRNDMVcrPEVPRMEELIPIFL 184
Cdd:PRK07740  59 LPFVVFDLETTGFSpQQGDEILSIGAVKTKGGevETDTFYSLVKPKrPIPEHILELTGITAEDV--AFAPPLAEVLHRFY 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  185 RYVESRqkpggyvMLVAHNGkSFDFQFLiNEFNRCSYEIPHNWLLLDSLPLarenMKSVEPTVKLsSSLEALADYYSLTR 264
Cdd:PRK07740 137 AFIGAG-------VLVAHHA-GHDKAFL-RHALWRTYRQPFTHRLIDTMFL----TKLLAHERDF-PTLDDALAYYGIPI 202

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 30690468  265 EGdAHRALSDVLLLSKVFQKLTIDLKlslsdlVLRCHTASDISAAMAK 312
Cdd:PRK07740 203 PR-RHHALGDALMTAKLWAILLVEAQ------QRGITTLHDLYAALSR 243
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 108-286 6.12e-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: 64.01  E-value: 6.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   108 LLTVIVSDLETTGlHRKNERIIEIAAQDIAGGGY--STFQTLVNPG-VVPITNAHIHGIRNDMVcrPEVPRMEELIPIFL 184
Cdd:TIGR00573   6 LDTETTGDNETTG-LYAGHDIIEIGAVEIINRRItgNKFHTYIKPDrPIDPDAIKIHGITDDML--KDKPDFKEIAEDFA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   185 RYVesrqkpGGYVmLVAHNGkSFDFQFLINEFNRCSYEIP--HNWLL-LDSLPLARENMKSVEPTvklsssLEALADYYS 261
Cdd:TIGR00573  83 DYI------RGAE-LVIHNA-SFDVGFLNYEFSKLYKVEPktNDVIDtTDTLQYARPEFPGKRNT------LDALCKRYE 148

                         170       180
                  ....*....|....*....|....*.
gi 30690468   262 LTREGDA-HRALSDVLLLSKVFQKLT 286
Cdd:TIGR00573 149 ITNSHRAlHGALADAFILAKLYLVMT 174
PRK08517 PRK08517
3'-5' exonuclease;
113-284 3.54e-10

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 59.27  E-value: 3.54e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  113 VSDLETTGLHRKNERIIEIAAQDIAGGG-YSTFQTLVNPGVVPITNAHIHGIRNDMVcrPEVPRMEELIP---IFLryve 188
Cdd:PRK08517  72 FVDIETNGSKPKKHQIIEIGAVKVKNGEiIDRFESFVKAKEVPEYITELTGITYEDL--ENAPSLKEVLEefrLFL---- 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  189 srqkpgGYVMLVAHNGKsFDFQFLINEFNRCSYEIPHNwLLLDSLPLARENMKSvePTVKLSSSLEALAdyyslTREGDA 268
Cdd:PRK08517 146 ------GDSVFVAHNVN-FDYNFISRSLEEIGLGPLLN-RKLCTIDLAKRTIES--PRYGLSFLKELLG-----IEIEVH 210

                        170
                 ....*....|....*.
gi 30690468  269 HRALSDVLLLSKVFQK 284
Cdd:PRK08517 211 HRAYADALAAYEIFKI 226
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 112-285 1.09e-09

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 56.57  E-value: 1.09e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 112 IVSDLETTGL-HRKNERIIEIA--AQDIAGGGYSTFQTLVNPGVV-----------PIT--NAHIHGIRNDMVCRpEVPR 175
Cdd:cd06136   2 VFLDLETTGLpKHNRPEITELClvAVHRDHLLNTSRDKPALPRVLdklslcfnpgrAISpgASEITGLSNDLLEH-KAPF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 176 MEELIPIFLRYVESRQKPggyVMLVAHNGKSFDFQFLINEFNRCSYEIPHNWLLLDSLPLAREnmksveptvkLSSSLEA 255
Cdd:cd06136  81 DSDTANLIKLFLRRQPKP---ICLVAHNGNRFDFPILRSELERLGTKLPDDILCVDSLPAFRE----------LDQSLGS 147

                       170       180       190
                ....*....|....*....|....*....|
gi 30690468 256 LADYYSLTREGDAHRALSDVLLLSKVFQKL 285
Cdd:cd06136 148 LYKRLFGQEPKNSHTAEGDVLALLKCALHK 177
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 112-311 5.40e-09

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 55.64  E-value: 5.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  112 IVSDLETTGL-HRKNERIIEIAAQDIAGGGYS--TFQTLVNPG--VVPITNAhIHGIRNDMVcrPEVPRMEELIPIFLRY 186
Cdd:PRK05711   7 IVLDTETTGLnQREGHRIIEIGAVELINRRLTgrNFHVYIKPDrlVDPEALA-VHGITDEFL--ADKPTFAEVADEFLDF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  187 VESRQkpggyvmLVAHNGkSFDFQFLINEFNRCSYEIPHNWLL---LDSLPLAREN--MKsveptvklSSSLEALADYYS 261
Cdd:PRK05711  84 IRGAE-------LIIHNA-PFDIGFMDYEFALLGRDIPKTNTFckvTDTLAMARRMfpGK--------RNSLDALCKRYG 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 30690468  262 LTregDAHR----ALSDVLLLSKVFQKLT---IDLKLSLSDLVLRCHTASDISAAMA 311
Cdd:PRK05711 148 ID---NSHRtlhgALLDAEILAEVYLAMTggqTSLGFAMEGETQQQQGEETIQRIVR 201
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 115-285 6.63e-09

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 55.37  E-value: 6.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  115 DLETTGLHRKNERIIE--IAAQDIAGGGYSTFQTLVNPGV-VPITNAHIHGIRNDMV---CRPEVPRMEELIPIfLRYVE 188
Cdd:PRK07942  12 DLETTGVDPETARIVTaaLVVVDADGEVVESREWLADPGVeIPEEASAVHGITTEYArahGRPAAEVLAEIADA-LREAW 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  189 SRQKPggyvmLVAHNGkSFDFQFLINEFNRCSYEIPHNWLLLDSLPLAREnmksVEPTVKLSSSLEALADYYSLTREGdA 268
Cdd:PRK07942  91 ARGVP-----VVVFNA-PYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKA----VDRYRKGKRTLTALCEHYGVRLDN-A 159

                        170
                 ....*....|....*..
gi 30690468  269 HRALSDVLLLSKVFQKL 285
Cdd:PRK07942 160 HEATADALAAARVAWAL 176
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 111-285 4.28e-08

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: 52.22  E-value: 4.28e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 111 VIVSDLETT------GLHRKNErIIEIAAQDI-AGGGY--STFQTLVNPGVVPITNAHI---HGIRNDMVcrPEVPRMEE 178
Cdd:cd06133   1 YLVIDFEATcwegnsKPDYPNE-IIEIGAVLVdVKTKEiiDTFSSYVKPVINPKLSDFCtelTGITQEDV--DNAPSFPE 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 179 LIPIFLRYVESRQKPGGYVMlvahnGKSFDFQFLINEFNRC---SYEIPHNWL-LLDSLPLARENMKSVeptvklssSLE 254
Cdd:cd06133  78 VLKEFLEWLGKNGKYAFVTW-----GDWDLKDLLQNQCKYKiinLPPFFRQWIdLKKEFAKFYGLKKRT--------GLS 144

                       170       180       190
                ....*....|....*....|....*....|.
gi 30690468 255 ALADYYSLTREGDAHRALSDVLLLSKVFQKL 285
Cdd:cd06133 145 KALEYLGLEFEGRHHRGLDDARNIARILKRL 175
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 143-274 2.62e-06

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: 46.35  E-value: 2.62e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 143 TFQTLVNPgvvPIT----NAHIHGIRNDMVCrpEVPRMEELIPIFLRYVESRqkpggyvMLVAHNgKSFDfqflINEFNR 218
Cdd:cd06130  32 TFYTLIRP---PTRfdpfNIAIHGITPEDVA--DAPTFPEVWPEIKPFLGGS-------LVVAHN-ASFD----RSVLRA 94

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30690468 219 C--SYEIP-HNWLLLDSLPLARENMKSVEPTvKLSSSLEALAdyYSLTRegdaHRALSD 274
Cdd:cd06130  95 AleAYGLPpPPYQYLCTVRLARRVWPLLPNH-KLNTVAEHLG--IELNH----HDALED 146
YprB COG3359
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ...
 98-267 6.15e-06

Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];


Pssm-ID: 442587 [Multi-domain]  Cd Length: 198  Bit Score: 46.09  E-value: 6.15e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  98 RLAQDKDLSKLLTVivsDLETTGLHRKNERIIEIAAQDIAGGGYSTFQTLV-NPGvvpitnahihgirndmvcrPEVPRM 176
Cdd:COG3359   7 FFAELLPSEDLLFF---DIETTGLSGGGTVIFLIGLADGEGDGFVVRQYFGeDPG-------------------EEAALL 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468 177 EELIPIFlryvesrqkpGGYVMLVAHNGKSFDFQFLINEF--NRCSYEIPHNWlLLDSLPLARENMKSVEPTVKLSSSLE 254
Cdd:COG3359  65 EAFLEWL----------ADYKLLVTYNGKSFDLPFLKTRFtlHRLPPPLPEFP-HLDLLHPARRLWKNRLPSGGLKTVEE 133

                       170
                ....*....|...
gi 30690468 255 ALadyySLTREGD 267
Cdd:COG3359 134 LL----GIEREDD 142
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 100-212 6.42e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 43.81  E-value: 6.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  100 AQDKDLSKLLTVIVSDLETTGL-HRKNErIIEIAAQ----DIAGGGYS---TFQTLVNPGV-VP--ITnaHIHGIRNDMV 168
Cdd:PRK09182  28 YPAPRGEFVRLGVILDTETTGLdPRKDE-IIEIGMVafeyDDDGRIGDvldTFGGLQQPSRpIPpeIT--RLTGITDEMV 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 30690468  169 CRPEVPRMEelipiflryVESRQKPGgyVMLVAHNGkSFDFQFL 212
Cdd:PRK09182 105 AGQTIDPAA---------VDALIAPA--DLIIAHNA-GFDRPFL 136
PRK09145 PRK09145
3'-5' exonuclease;
111-286 3.43e-04

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 41.04  E-value: 3.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  111 VIVSDLETTGLHRKNERIIEIAAQDIAGGGYSTFQTL---VNPGVVPITNA-HIHGIRN-DMVcrpEVPRMEELIPIFLR 185
Cdd:PRK09145  31 WVALDCETTGLDPRRAEIVSIAAVKIRGNRILTSERLellVRPPQSLSAESiKIHRLRHqDLE---DGLSEEEALRQLLA 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468  186 YVESRQKPGGYVmlvahngkSFDFQFLinefNR-----CSYEIPHNwlLLDSLPLARENMKSVEPTVKLSSSLEALADYY 260
Cdd:PRK09145 108 FIGNRPLVGYYL--------EFDVAML----NRyvrplLGIPLPNP--LIEVSALYYDKKERHLPDAYIDLRFDAILKHL 173

                        170       180
                 ....*....|....*....|....*.
gi 30690468  261 SLTrEGDAHRALSDVLLLSKVFQKLT 286
Cdd:PRK09145 174 DLP-VLGRHDALNDAIMAALIFLRLR 198
RNase_H_2 pfam13482
RNase_H superfamily;
115-267 4.14e-04

RNase_H superfamily;


Pssm-ID: 433246 [Multi-domain]  Cd Length: 163  Bit Score: 40.27  E-value: 4.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   115 DLETTGLHRKNERIIEIAAQDIAGGGYSTFQTLVNPGvvpitnahihgirndmvcRPEVPRMEELIPIFLRYVesrqkpg 194
Cdd:pfam13482   4 DIETTGLSPGKNTIYLIGVYDVDGDKVRTFVQYLAEG------------------PTEEAAILQLFELLADYP------- 58

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30690468   195 gyvMLVAHNGKSFDFQFLINEFNR--CSYEIPHnwllLDSLPLARENmksveptvKLSSSLEALADYYSLTREGD 267
Cdd:pfam13482  59 ---LLVTFNGKSFDVPFIKRRFKRydLDELFRH----IDLLHPLRKL--------GLESGLKSVERELGIERRDD 118
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 77-235 4.16e-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: 38.54  E-value: 4.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468    77 VTRIIDEESRTKVQPFGNlqqRLAQDKdlsklltVIVSDLETTGLHRKNERIIEIAAQDIAGGGY--STFQTLVNPgVVP 154
Cdd:pfam13361 164 LSDFINPDTLTYGDPFVI---ALEQDN-------IVVFDVETTGLDTTEDEIIQIAAIKLNKKGVviESFERFLRL-KKP 232

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690468   155 ITNA-HIHGIRNDMVCRPEVP-------------RMEELIPIFlRYVESRQKPGGYVMLVAHngksfdfqflINEFNRCS 220
Cdd:pfam13361 233 VGDSlQVHGFSDEFLQENGETpaealrdflekleNLRELYSIL-REYDDIEETPEPEDALRN----------FLEIATLS 301

                         170
                  ....*....|....*
gi 30690468   221 YEIPHNWLLLDSLPL 235
Cdd:pfam13361 302 NSELEGSDIKERIPI 316
Orn COG1949
Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];
115-133 7.47e-03

Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification];


Pssm-ID: 441552  Cd Length: 177  Bit Score: 36.62  E-value: 7.47e-03
                        10
                ....*....|....*....
gi 30690468 115 DLETTGLHRKNERIIEIAA 133
Cdd:COG1949   8 DLEMTGLDPETDRIIEIAT 26
PRK05359 PRK05359
oligoribonuclease; Provisional
 115-133 8.07e-03

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 36.67  E-value: 8.07e-03
                         10
                 ....*....|....*....
gi 30690468  115 DLETTGLHRKNERIIEIAA 133
Cdd:PRK05359   9 DLEMTGLDPERDRIIEIAT 27
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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