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Conserved domains on  [gi|446449050|ref|WP_000526905|]
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MULTISPECIES: 3'-5' exonuclease [Bacillus]

Protein Classification

3'-5' exonuclease( domain architecture ID 11482424)

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
PRK06807 PRK06807
3'-5' exonuclease;
1-313 0e+00

3'-5' exonuclease;


:

Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 572.14  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:PRK06807   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160
Cdd:PRK06807  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050 161 CAAVYQKCASIEEEAKKKSNTEVLDETAVYEAVKEILVRNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240
Cdd:PRK06807 161 CAAVYQKCASIEEEAKRKSNKEVLDETAVYEAVKEILVKNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446449050 241 LEDDVKEICTSLACEPALKSEVGNTRIMLNCLEDVLKLESYILEQYDFVLQALHDYKQSEMNADEKLKEYLNI 313
Cdd:PRK06807 241 LEDDVKEICTSLKCEPALKSEVGNTRIMLNSLEDVLKLESYILEQYDFVLQALHDYKNNEMNADEKLKEYLNI 313
 
Name Accession Description Interval E-value
PRK06807 PRK06807
3'-5' exonuclease;
1-313 0e+00

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 572.14  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:PRK06807   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160
Cdd:PRK06807  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050 161 CAAVYQKCASIEEEAKKKSNTEVLDETAVYEAVKEILVRNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240
Cdd:PRK06807 161 CAAVYQKCASIEEEAKRKSNKEVLDETAVYEAVKEILVKNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446449050 241 LEDDVKEICTSLACEPALKSEVGNTRIMLNCLEDVLKLESYILEQYDFVLQALHDYKQSEMNADEKLKEYLNI 313
Cdd:PRK06807 241 LEDDVKEICTSLKCEPALKSEVGNTRIMLNSLEDVLKLESYILEQYDFVLQALHDYKNNEMNADEKLKEYLNI 313
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-168 4.59e-75

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 228.10  E-value: 4.59e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:COG2176    1 MSLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPePKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCI 159
Cdd:COG2176   81 EFLEFLGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDrHRALGDAE 159


                 ....*....
gi 446449050 160 TCAAVYQKC 168
Cdd:COG2176  160 ATAELFLKL 168
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-166 3.86e-59

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: 186.74  E-value: 3.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYNDKIIQVAAVKYRNH-ELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446449050  90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKR-MLGIRLS-SHNAFDDCITCAAVYQ 166
Cdd:cd06127   81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAeRYGIPLEgAHRALADALATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 10-173 1.00e-47

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 157.85  E-value: 1.00e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050    10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050    90 VIVAHN-ASFDMRFLKSNVNMLGLPEP-KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS--HNAFDDCITCAAVY 165
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPpKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQraHRALDDARATAKLF 161


                   ....*...
gi 446449050   166 QKCASIEE 173
Cdd:smart00479 162 KKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 11-165 5.01e-33

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: 119.76  E-value: 5.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   11 VVIDFETTGFNPYNDKIIQVAAVKYRNHELV--DQFVSYVNPERP--IPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEigETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   87 HT-NVIVAHNASFDMRFLKSN--VNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS--SHNAFDDCITC 161
Cdd:pfam00929  81 RKgNLLVAHNASFDVGFLRYDdkRFLKKPMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRALDDARAT 160


                  ....
gi 446449050  162 AAVY 165
Cdd:pfam00929 161 AKLF 164
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 10-162 2.41e-31

DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 123.76  E-value: 2.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:TIGR01407   2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446449050   90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCA 162
Cdd:TIGR01407  82 IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHEnPHRADSDAQATA 155
 
Name Accession Description Interval E-value
PRK06807 PRK06807
3'-5' exonuclease;
1-313 0e+00

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 572.14  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:PRK06807   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160
Cdd:PRK06807  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCIT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050 161 CAAVYQKCASIEEEAKKKSNTEVLDETAVYEAVKEILVRNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240
Cdd:PRK06807 161 CAAVYQKCASIEEEAKRKSNKEVLDETAVYEAVKEILVKNKRDIEWIRCMNVGSYLDIKAFYPVMRLKVKGRKKYVLTDI 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446449050 241 LEDDVKEICTSLACEPALKSEVGNTRIMLNCLEDVLKLESYILEQYDFVLQALHDYKQSEMNADEKLKEYLNI 313
Cdd:PRK06807 241 LEDDVKEICTSLKCEPALKSEVGNTRIMLNSLEDVLKLESYILEQYDFVLQALHDYKNNEMNADEKLKEYLNI 313
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-168 4.59e-75

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 228.10  E-value: 4.59e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   1 MGNISLPLDYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:COG2176    1 MSLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPePKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDDCI 159
Cdd:COG2176   81 EFLEFLGDAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDrHRALGDAE 159


                 ....*....
gi 446449050 160 TCAAVYQKC 168
Cdd:COG2176  160 ATAELFLKL 168
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 9-167 1.91e-64

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 200.40  E-value: 1.91e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  89 NVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAVYQK 167
Cdd:COG0847   81 AVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDeRHRALADAEATAELFLA 160
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-166 3.86e-59

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: 186.74  E-value: 3.86e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYNDKIIQVAAVKYRNH-ELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446449050  90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKR-MLGIRLS-SHNAFDDCITCAAVYQ 166
Cdd:cd06127   81 VLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAeRYGIPLEgAHRALADALATAELLL 159
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
6-158 1.84e-51

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 178.19  E-value: 1.84e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   6 LPLD---YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82
Cdd:PRK07883  10 TPLRdvtFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAF 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446449050  83 LAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYM--KHAPNHKLETLKRMLGIRLS-SHNAFDDC 158
Cdd:PRK07883  90 LEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLprDEAPNVRLSTLARLFGATTTpTHRALDDA 168
polC PRK00448
DNA polymerase III PolC; Validated
 10-201 2.62e-51

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 181.96  E-value: 2.62e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:PRK00448  421 YVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRL-SSHNAFDDCITCAAVYQKC 168
Cdd:PRK00448  501 ILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELeHHHRADYDAEATAYLLIKF 580

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 446449050  169 asiEEEAKKKS-------NTEVLDETA-----VYEAVkeILVRNK 201
Cdd:PRK00448  581 ---LKDLKEKGitnldelNKKLGSEDAykkarPKHAT--ILVKNQ 620
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 10-173 1.00e-47

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 157.85  E-value: 1.00e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050    10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050    90 VIVAHN-ASFDMRFLKSNVNMLGLPEP-KNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS--HNAFDDCITCAAVY 165
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPpKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQraHRALDDARATAKLF 161


                   ....*...
gi 446449050   166 QKCASIEE 173
Cdd:smart00479 162 KKLLERLE 169
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 10-165 8.18e-40

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: 136.87  E-value: 8.18e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:cd06130    1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446449050  90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCAAVY 165
Cdd:cd06130   79 LVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNHHDALEDARACAEIL 154
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 10-148 2.33e-39

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 147.41  E-value: 2.33e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPY-NDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
Cdd:PRK08074   5 FVVVDLETTGNSPKkGDKIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEG 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  89 NVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIR 148
Cdd:PRK08074  85 AYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLE 144
PRK08517 PRK08517
3'-5' exonuclease;
9-168 1.13e-35

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 129.37  E-value: 1.13e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERpIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88
Cdd:PRK08517  69 VFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKE-VPEYITELTGITYEDLENAPSLKEVLEEFRLFLGD 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  89 NVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKhAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAVYQK 167
Cdd:PRK08517 148 SVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIE-SPRYGLSFLKELLGIEIEvHHRAYADALAAYEIFKI 226


                 .
gi 446449050 168 C 168
Cdd:PRK08517 227 C 227
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 10-165 1.57e-33

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: 121.10  E-value: 1.57e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPY-NDKIIQVAAVkyrnhELVD------QFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82
Cdd:cd06131    1 QIVLDTETTGLDPReGHRIIEIGCV-----ELINrrltgnTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  83 LAFLHTNVIVAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMKHAPNhKLETLKRMLGIRLSS---HNAFD 156
Cdd:cd06131   76 LDFIRGAELVIHNASFDVGFLNAELSLLGLGkkiIDFCRVIDTLALARKKFPGKPN-SLDALCKRFGIDNSHrtlHGALL 154


                 ....*....
gi 446449050 157 DCITCAAVY 165
Cdd:cd06131  155 DAELLAEVY 163
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 11-165 5.01e-33

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: 119.76  E-value: 5.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   11 VVIDFETTGFNPYNDKIIQVAAVKYRNHELV--DQFVSYVNPERP--IPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGENEigETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   87 HT-NVIVAHNASFDMRFLKSN--VNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS--SHNAFDDCITC 161
Cdd:pfam00929  81 RKgNLLVAHNASFDVGFLRYDdkRFLKKPMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIgrAHRALDDARAT 160


                  ....
gi 446449050  162 AAVY 165
Cdd:pfam00929 161 AKLF 164
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 10-162 2.41e-31

DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 123.76  E-value: 2.41e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:TIGR01407   2 YAVVDLETTGTQLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446449050   90 VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCA 162
Cdd:TIGR01407  82 IFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHEnPHRADSDAQATA 155
PRK07740 PRK07740
hypothetical protein; Provisional
 8-157 1.86e-30

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 115.15  E-value: 1.86e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   8 LDYVVIDFETTGFNPYN-DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAF 85
Cdd:PRK07740  59 LPFVVFDLETTGFSPQQgDEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF 138

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446449050  86 LHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSS-HNAFDD 157
Cdd:PRK07740 139 IGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRrHHALGD 211
PRK06063 PRK06063
DEDDh family exonuclease;
7-164 6.50e-27

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 107.48  E-value: 6.50e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   7 PLDYVVIDFETTGFNPYNDKIIQVAAVKYR-NHELVDQFVSYVNPER-PIPdriTSLTGITNYRVSDAPTIEEVLPLFLA 84
Cdd:PRK06063  14 PRGWAVVDVETSGFRPGQARIISLAVLGLDaDGNVEQSVVTLLNPGVdPGP---THVHGLTAEMLEGQPQFADIAGEVAE 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  85 FLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGI-RLSSHNAFDDCITCAA 163
Cdd:PRK06063  91 LLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVpQQRPHDALDDARVLAG 170


                 .
gi 446449050 164 V 164
Cdd:PRK06063 171 I 171
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 14-167 2.46e-26

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 104.12  E-value: 2.46e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  14 DFETTGFNPYNDKIIQVAAVkyrNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTNVI-V 92
Cdd:PRK06309   8 DTETTGTQIDKDRIIEIAAY---NGVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNIlV 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446449050  93 AHNA-SFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAVYQK 167
Cdd:PRK06309  85 AHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENqAHRALDDVITLHRVFSA 161
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 10-166 2.48e-25

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 101.83  E-value: 2.48e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL-HT 88
Cdd:PRK06310   9 FVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFkEG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  89 NVIVAHNASFDMRFLKSNVNMLGLP--EPKNKVIDTVFLAKKYmKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAVY 165
Cdd:PRK06310  89 DYIVGHSVGFDLQVLSQESERIGETflSKHYYIIDTLRLAKEY-GDSPNNSLEALAVHFNVPYDgNHRAMKDVEINIKVF 167


                 .
gi 446449050 166 Q 166
Cdd:PRK06310 168 K 168
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 10-166 5.90e-24

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: 97.14  E-value: 5.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:TIGR00573   9 ETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   90 VIVAHNASFDMRFLKSNVNMLGLPEPK-NKVIDTVFLAKKYMKHAPNHK--LETLKRMLGIRLSS---HNAFDDCITCAA 163
Cdd:TIGR00573  89 ELVIHNASFDVGFLNYEFSKLYKVEPKtNDVIDTTDTLQYARPEFPGKRntLDALCKRYEITNSHralHGALADAFILAK 168


                  ...
gi 446449050  164 VYQ 166
Cdd:TIGR00573 169 LYL 171
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 8-181 2.35e-22

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 94.85  E-value: 2.35e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   8 LDYVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPE--RPIPDRItSLTGITNYRVSDAPTIEEVLPLFLAF 85
Cdd:PRK06195   1 MNFVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKemRFMPINI-GIHGIRPHMVEDELEFDKIWEKIKHY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  86 LHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCAAVY 165
Cdd:PRK06195  78 FNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSNIL 157

                        170       180
                 ....*....|....*....|..
gi 446449050 166 ------QKCASIEEEAKKKSNT 181
Cdd:PRK06195 158 lniskeLNSKDINEISKLLGVT 179
PRK07247 PRK07247
3'-5' exonuclease;
9-167 2.67e-22

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 92.15  E-value: 2.67e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   9 DYVVIDFEttgFNPYNDK--IIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86
Cdd:PRK07247   6 TYIAFDLE---FNTVNGVshIIQVSAVKYDDHKEVDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFKEFV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  87 HTNVIVAHNAsfdmrfLKSNV-----NMLGLPEP-KNKVIDTVFLAKKYMKHA-PNHKLETLKRMLGIRLSSHNAFDDCI 159
Cdd:PRK07247  83 GELPLIGYNA------QKSDLpilaeNGLDLSDQyQVDLYDEAFERRSSDLNGiANLKLQTVADFLGIKGRGHNSLEDAR 156


                 ....*...
gi 446449050 160 TCAAVYQK 167
Cdd:PRK07247 157 MTARVYES 164
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 10-168 4.92e-22

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: 90.74  E-value: 4.92e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETT-GFNPYNDK----IIQVAAVKY--RNHELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEEVLP 80
Cdd:cd06133    1 YLVIDFEATcWEGNSKPDypneIIEIGAVLVdvKTKEIIDTFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  81 LFLAFLHTNVIVAhNASF---DMRFLKSN---VNMLGLPEPKNKVIDtvfLAKKYMKHAPNHKLETLKRML---GIRLSS 151
Cdd:cd06133   81 EFLEWLGKNGKYA-FVTWgdwDLKDLLQNqckYKIINLPPFFRQWID---LKKEFAKFYGLKKRTGLSKALeylGLEFEG 156

                        170
                 ....*....|....*....
gi 446449050 152 --HNAFDDCITCAAVYQKC 168
Cdd:cd06133  157 rhHRGLDDARNIARILKRL 175
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 10-174 2.85e-21

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 94.37  E-value: 2.85e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPyNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTN 89
Cdd:PRK07246   9 YAVVDLEATGAGP-NASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  90 VIVAHNASFDMRFLKSNVNMLGLpEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAVY--- 165
Cdd:PRK07246  88 IFVAHNVKFDANLLAEALFLEGY-ELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLAdAHTAIADARATAELFlkl 166

                        170
                 ....*....|
gi 446449050 166 -QKCASIEEE 174
Cdd:PRK07246 167 lQKIESLPKE 176
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 11-128 4.38e-19

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 84.53  E-value: 4.38e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYN-DKIIQVAAVkyrnhELVDQFVS------YVNPERPI-PDRItSLTGITNYRVSDAPTIEEVLPLF 82
Cdd:PRK05711   7 IVLDTETTGLNQREgHRIIEIGAV-----ELINRRLTgrnfhvYIKPDRLVdPEAL-AVHGITDEFLADKPTFAEVADEF 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446449050  83 LAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN----KVIDTVFLAKK 128
Cdd:PRK05711  81 LDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTntfcKVTDTLAMARR 130
PRK09145 PRK09145
3'-5' exonuclease;
10-167 3.74e-18

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 81.10  E-value: 3.74e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPYNDKIIQVAAVKYRNHELV--DQFVSYVNPERPI-PDRITsLTGITNYRVSDAPTIEEVLPLFLAFL 86
Cdd:PRK09145  31 WVALDCETTGLDPRRAEIVSIAAVKIRGNRILtsERLELLVRPPQSLsAESIK-IHRLRHQDLEDGLSEEEALRQLLAFI 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  87 HTNVIVAHNASFDMRFL-KSNVNMLGLPEPkNKVID--TVFLAKKYmKHAPNHK----LETLKRMLGI-RLSSHNAFDDC 158
Cdd:PRK09145 110 GNRPLVGYYLEFDVAMLnRYVRPLLGIPLP-NPLIEvsALYYDKKE-RHLPDAYidlrFDAILKHLDLpVLGRHDALNDA 187


                 ....*....
gi 446449050 159 ITCAAVYQK 167
Cdd:PRK09145 188 IMAALIFLR 196
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 11-103 9.23e-18

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 81.95  E-value: 9.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYNDKIIQVAAVKY------RNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDApTIE-EVLPLFL 83
Cdd:PRK09182  40 VILDTETTGLDPRKDEIIEIGMVAFeydddgRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQ-TIDpAAVDALI 118

                         90       100
                 ....*....|....*....|
gi 446449050  84 AflHTNVIVAHNASFDMRFL 103
Cdd:PRK09182 119 A--PADLIIAHNAGFDRPFL 136
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 12-163 2.25e-13

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 68.21  E-value: 2.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  12 VIDFETTGFNpynDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAflhTNVI 91
Cdd:PRK07983   4 VIDTETCGLQ---GGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYG---SEWY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  92 VAHNASFDMRFlksnvnmlgLPEPKNKVIDTVFLAKKYMkhaPNHKL--ETLKRMLGIR------LSSHNAFDDCITCAA 163
Cdd:PRK07983  78 VAHNASFDRRV---------LPEMPGEWICTMKLARRLW---PGIKYsnMALYKSRKLNvqtppgLHHHRALYDCYITAA 145
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 9-166 1.02e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 63.79  E-value: 1.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   9 DYVVIDFETTGFNPYNDKIIQVAAVKYrNHELVdqFVS-----YVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83
Cdd:PRK09146  48 PFVALDFETTGLDAEQDAIVSIGLVPF-TLQRI--RCRqarhwVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELL 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  84 AFLHTNVIVAHNASFDMRFLKSNVNML---GLPEPknkVIDTVFLAKKYMKHAPNHKLETLK--RMLGIRL--------- 149
Cdd:PRK09146 125 EALAGKVVVVHYRRIERDFLDQALRNRigeGIEFP---VIDTMEIEARIQRKQAGGLWNRLKgkKPESIRLadsrlrygl 201

                        170       180
                 ....*....|....*....|
gi 446449050 150 ---SSHNAFDDCITCAAVYQ 166
Cdd:PRK09146 202 paySPHHALTDAIATAELLQ 221
PRK07748 PRK07748
3'-5' exonuclease KapD;
9-165 3.07e-10

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 58.93  E-value: 3.07e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   9 DYVVIDFETT---------GFNPyndKIIQVAAVKYRNHELVDQFVSYVNPER--PIPDRITSLTGITNYRVSDAPTIEE 77
Cdd:PRK07748   5 QFLFLDFEFTmpqhkkkpkGFFP---EIIEVGLVSVVGCEVEDTFSSYVKPKTfpSLTERCKSFLGITQEDVDKGISFEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  78 VLPLFLAFLH---TNVIVAHNAsfDMRFLKSNVNMLGLPEP-KNKVIDtvfLAKKYMKHAPNHKLETLKRML-------- 145
Cdd:PRK07748  82 LVEKLAEYDKrckPTIVTWGNM--DMKVLKHNCEKAGVPFPfKGQCRD---LSLEYKKFFGERNQTGLWKAIeeygkegt 156

                        170       180
                 ....*....|....*....|
gi 446449050 146 GIRlssHNAFDDCITCAAVY 165
Cdd:PRK07748 157 GKH---HCALDDAMTTYNIF 173
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 11-166 5.50e-09

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: 54.21  E-value: 5.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYNDKIIQVAAVKYRNHE-LVDQFVSyvnPERPIPDRITSLTGITNYRVSDAPTIEEVLP-------LF 82
Cdd:cd06137    1 VALDCEMVGLADGDSEVVRISAVDVLTGEvLIDSLVR---PSVRVTDWRTRFSGVTPADLEEAAKAGKTIFgweaaraAL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  83 LAFL--HTnVIVAHNASFDMRFLKsnvnmlglpEPKNKVIDTVFLAKKY---MKHAPNHKLETL-KRMLGIRL----SSH 152
Cdd:cd06137   78 WKFIdpDT-ILVGHSLQNDLDALR---------MIHTRVVDTAILTREAvkgPLAKRQWSLRTLcRDFLGLKIqgggEGH 147

                        170
                 ....*....|....
gi 446449050 153 NAFDDCITCAAVYQ 166
Cdd:cd06137  148 DSLEDALAAREVVL 161
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 14-203 2.43e-08

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 53.83  E-value: 2.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  14 DFETTGFNPYNDKIIQVAAVKYRNH-ELVDQFVSYVNPERPIPDRITSLTGITNYRVSD-----APTIEEVLPLFLAFLH 87
Cdd:PRK07942  12 DLETTGVDPETARIVTAALVVVDADgEVVESREWLADPGVEIPEEASAVHGITTEYARAhgrpaAEVLAEIADALREAWA 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  88 TNV-IVAHNASFDMRFLKSNVNMLGLPEPKN-KVIDTVFLAKKYMKHAP-NHKLETLKRMLGIRL-SSHNAFDDCITCAA 163
Cdd:PRK07942  92 RGVpVVVFNAPYDLTVLDRELRRHGLPSLVPgPVIDPYVIDKAVDRYRKgKRTLTALCEHYGVRLdNAHEATADALAAAR 171

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446449050 164 VYQKCASIEEEAKKKSNTEVLDETAVYEAV-----KEILVRNKRD 203
Cdd:PRK07942 172 VAWALARRFPELAALSPAELHELQAVWYAEqaasfQAYLRRKGRP 216
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 29-166 2.29e-07

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: 49.44  E-value: 2.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  29 QVAAVKYRNHELVDqfvSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHTNVIVAHNASFDMRflksnvn 108
Cdd:cd06144   21 RVSIVNEDGNVVYD---TYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGHALKNDLK------- 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446449050 109 MLGLPEPKNKVIDTVfLAKKYMKHAPNHK--LETL-KRMLGIRLS--SHNAFDDCITCAAVYQ 166
Cdd:cd06144   91 VLKLDHPKKLIRDTS-KYKPLRKTAKGKSpsLKKLaKQLLGLDIQegEHSSVEDARAAMRLYR 152
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 9-162 2.34e-07

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: 50.12  E-value: 2.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050    9 DYVVIDFETTGFNPyNDKIIQVAAVKYR--NHELVDQFVSYVNPE-------RPIPDRIT-----SLTGITNYRVSDAPT 74
Cdd:pfam16473   1 NHLMIDIETLGNEP-TAPIVSIGAVFFDpeTGELGKEFYARIDLEssmsagaTIDADTILwwlkqSSEARAQLLGDDAPS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   75 IEEVLPLFLAFLHTN------VIVAHNASFDMRFLKSNVNMLGLPEPknkvidtvflakkyMKHAPNHKLETLKRM---L 145
Cdd:pfam16473  80 LPDALLDLNDFIRDNgdpkslKVWGNGASFDNVILRAAFERGGLPAP--------------WKYWNDRDVRTIVALgpeL 145

                         170       180
                  ....*....|....*....|....*
gi 446449050  146 GIRLSS--------HNAFDDCITCA 162
Cdd:pfam16473 146 GYDPKRdipfegvkHNALDDAIHQA 170
PRK06722 PRK06722
exonuclease; Provisional
 10-195 3.07e-07

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 50.82  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTgFNPYND----KIIQVAAVKYR--NHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFL 83
Cdd:PRK06722   7 FIVFDIERN-FRPYKSedpsEIVDIGAVKIEasTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQIIEKFI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  84 AFLHTNVIVAHNASFDMRFLKSNVNMLGLPEP---KNKVIDT---VFLA-KKYMKHAPNhkLETLKRMLGIRLS--SHNA 154
Cdd:PRK06722  86 QFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPcmeKERRIDLqkfVFQAyEELFEHTPS--LQSAVEQLGLIWEgkQHRA 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 446449050 155 FDDCITCAAVYQKCAS---IEEEAKKKSNTEVLDETAVYEAVKE 195
Cdd:PRK06722 164 LADAENTANILLKAYSerdITKRYKRHGELELVKNGKLTEKAKK 207
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 11-126 2.35e-06

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 47.29  E-value: 2.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  11 VVIDFETTGFNPYNDKIIQVAAVKYRNHE----LVDQFVSY-VNP-ERPIPDRiTSL--TGITNYR-----VSDAPTIEE 77
Cdd:cd06134    8 VVVDVETGGFNPQTDALLEIAAVTLEMDEqgnlYPDETFHFhILPfEGANLDP-AALefNGIDPFHpfrfaVDEKEALKE 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446449050  78 VLPLFLAFLHTN-----VIVAHNASFDMRFLKSNVNMLGLpePKN-----KVIDTVFLA 126
Cdd:cd06134   87 IFKPIRKALKAQgctraILVGHNAHFDLGFLNAAVARCKI--KRNpfhpfSTFDTATLA 143
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 10-165 3.16e-06

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: 46.56  E-value: 3.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  10 YVVIDFETTGFNPYND-KIIQVAAVKY-RNH------------ELVDQFVSYVNPERPIPDRITSLTGITNYRVSD-APT 74
Cdd:cd06136    1 FVFLDLETTGLPKHNRpEITELCLVAVhRDHllntsrdkpalpRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHkAPF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  75 IEEVLPLFLAFLHTN----VIVAHNAS-FDMRFLKSNVNMLGLPEPKNKV-IDTVFLAKKYmkhapNHKLETL-KRMLGI 147
Cdd:cd06136   81 DSDTANLIKLFLRRQpkpiCLVAHNGNrFDFPILRSELERLGTKLPDDILcVDSLPAFREL-----DQSLGSLyKRLFGQ 155

                        170       180
                 ....*....|....*....|..
gi 446449050 148 R-LSSHNAFDDC---ITCAAVY 165
Cdd:cd06136  156 EpKNSHTAEGDVlalLKCALHK 177
UvrD_C pfam13361
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 11-58 7.44e-06

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: 47.02  E-value: 7.44e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 446449050   11 VVIDFETTGFNPYNDKIIQVAAVKYRNH-ELVDQFVSYVNPERPIPDRI 58
Cdd:pfam13361 189 VVFDVETTGLDTTEDEIIQIAAIKLNKKgVVIESFERFLRLKKPVGDSL 237
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 7-89 1.28e-04

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 43.34  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050   7 PLD-YVVIDFETT---GFNPYNDKIIQ--VAAVKYRNHELVDQFVSYVNP-ERPIPDRI-TSLTGITNYRVSDAPTIEEV 78
Cdd:PTZ00315  54 PFDaYVVLDFEATceaDRRIEDAEVIEfpMVLVDARTATPVAEFQRYVRPvKNPVLSRFcTELTGITQSMVSRADPFPVV 133

                         90
                 ....*....|.
gi 446449050  79 LPLFLAFLHTN 89
Cdd:PTZ00315 134 YCEALQFLAEA 144
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 47-161 2.14e-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: 37.85  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446449050  47 YVNPERPIPDRITSLTGITNYRVSDAP-TIEEVLPLFLAFLHTN-VIVAHNASFDMRFLKsnvnMLglpepKNKVIDTV- 123
Cdd:cd06145   33 LVKPDGEIVDYNTRFSGITEEMLENVTtTLEDVQKKLLSLISPDtILVGHSLENDLKALK----LI-----HPRVIDTAi 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446449050 124 ---------------FLAKKYmkhapnhkletLKRMLGIRLSSHNAFDDCITC 161
Cdd:cd06145  104 lfphprgppykpslkNLAKKY-----------LGRDIQQGEGGHDSVEDARAA 145
PRK05359 PRK05359
oligoribonuclease; Provisional
 13-33 9.32e-03

oligoribonuclease; Provisional


Pssm-ID: 235429  Cd Length: 181  Bit Score: 36.29  E-value: 9.32e-03
                         10        20
                 ....*....|....*....|.
gi 446449050  13 IDFETTGFNPYNDKIIQVAAV 33
Cdd:PRK05359   8 IDLEMTGLDPERDRIIEIATI 28
 
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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