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Conserved domains on  [gi|240254568|ref|NP_850189|]
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Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [Arabidopsis thaliana]

Protein Classification

RRP6 family protein( domain architecture ID 10150260)

RRP6 family protein may be involved in the degradation of aberrant transcripts and processing of precursors to stable RNAs

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 115-308 3.70e-102

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


:

Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 315.31  E-value: 3.70e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 240254568 275 LLYIADSLTTELKQLatDSSSPDDRFHFLLEASR 308
Cdd:cd06147  161 LLYIYDRLRNELLER--ANALAPNLLESVLNCSR 192
HRDC super family cl02578
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 353-396 3.03e-07

HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.


The actual alignment was detected with superfamily member pfam00570:

Pssm-ID: 470625 [Multi-domain]  Cd Length: 68  Bit Score: 48.30  E-value: 3.03e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 240254568  353 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 396
Cdd:pfam00570   2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEE 45
 
Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 115-308 3.70e-102

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 315.31  E-value: 3.70e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 240254568 275 LLYIADSLTTELKQLatDSSSPDDRFHFLLEASR 308
Cdd:cd06147  161 LLYIYDRLRNELLER--ANALAPNLLESVLNCSR 192
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 119-287 7.74e-61

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 204.07  E-value: 7.74e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLR--SFLGFTALIQISTHEEDFLVDTIALHD-VMSILRPVFSDPNICKV 195
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDdVLSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  196 FHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQ-RSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
gi 240254568  275 LLYIADSLTTELK 287
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
121-397 4.53e-52

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 186.62  E-value: 4.53e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSF---LGftaLIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFH 197
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYyprLC---LIQLADGEEVALIDPLAIGD-LSPLWELLADPAIVKVFH 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 198 GADNDVIWLQRDFHIYVVNMFDTAKACEVLS-KPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLL 276
Cdd:COG0349   77 AAREDLEILYHLFGILPKPLFDTQIAAALLGyGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 277 YIADSLTTELKQLatdssspdDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL- 355
Cdd:COG0349  157 PLYEKLLEELERE--------GRLEWAEEECAR--LLDPATYREDPEE----------AWLRL-----KGAWKLNPRQLa 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 240254568 356 -VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEI 397
Cdd:COG0349  212 vLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEEL 254
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 119-286 7.14e-35

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 130.94  E-value: 7.14e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568   119 YVWVETESQLKELAEILAKEQ-VFAVDTEQHSLRSFLGFTALIQISTH-EEDFLVDTIALHDVMSILRPVFSDPNICKVF 196
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGgEVALDTETTGLDSYSGKLVLIQISVTgEGAFIIDPLALGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568   197 HGADNDVIWLQRdFHIYVVNMFDTAKACEVLSKPQR--SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSkhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 240254568   275 LLYIADSLTTEL 286
Cdd:smart00474 160 LLRLYEKLEKEL 171
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 121-452 1.51e-26

ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]


Pssm-ID: 130455 [Multi-domain]  Cd Length: 367  Bit Score: 112.56  E-value: 1.51e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGAD 200
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKVLHAAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  201 NDVIWLQRDFHIYVVNMFDTAKACEVLSKPQrSLAY--LLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYI 278
Cdd:TIGR01388  80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGM-SMGYakLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  279 ADSLTTELKQlatdssspDDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL--V 356
Cdd:TIGR01388 159 YAKLMERLEE--------SGRLAWLEEECTL--LTDRRTYVVNPED----------AWRDI-----KNAWQLRPQQLavL 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  357 RKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEiydtiahidLATESSPSLSssvqspypvICSHLDDIYKMI 436
Cdd:TIGR01388 214 QALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTE---------LASLGPKGSE---------IRKHGDTLLALV 275

                         330
                  ....*....|....*.
gi 240254568  437 LDKLAKLDDLLPVVLK 452
Cdd:TIGR01388 276 KTALALPEDALPQAPL 291
PRK10829 PRK10829
ribonuclease D; Provisional
 119-288 2.08e-12

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 69.65  E-value: 2.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHG 198
Cdd:PRK10829   3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQVTKFLHA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRS-LAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLY 277
Cdd:PRK10829  82 GSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCgFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLP 161

                        170
                 ....*....|.
gi 240254568 278 IADSLTTELKQ 288
Cdd:PRK10829 162 IAAKLMAETEA 172
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 353-396 3.03e-07

HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.


Pssm-ID: 425755 [Multi-domain]  Cd Length: 68  Bit Score: 48.30  E-value: 3.03e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 240254568  353 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 396
Cdd:pfam00570   2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEE 45
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 351-398 1.12e-05

Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.


Pssm-ID: 128635 [Multi-domain]  Cd Length: 81  Bit Score: 44.21  E-value: 1.12e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 240254568   351 NAEELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEIY 398
Cdd:smart00341   3 RQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELL 50
 
Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 115-308 3.70e-102

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 315.31  E-value: 3.70e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                        170       180       190
                 ....*....|....*....|....*....|....
gi 240254568 275 LLYIADSLTTELKQLatDSSSPDDRFHFLLEASR 308
Cdd:cd06147  161 LLYIYDRLRNELLER--ANALAPNLLESVLNCSR 192
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 119-287 7.74e-61

3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.


Pssm-ID: 396266 [Multi-domain]  Cd Length: 173  Bit Score: 204.07  E-value: 7.74e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLR--SFLGFTALIQISTHEEDFLVDTIALHD-VMSILRPVFSDPNICKV 195
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDdVLSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  196 FHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQ-RSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
gi 240254568  275 LLYIADSLTTELK 287
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
121-397 4.53e-52

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 186.62  E-value: 4.53e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSF---LGftaLIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFH 197
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYyprLC---LIQLADGEEVALIDPLAIGD-LSPLWELLADPAIVKVFH 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 198 GADNDVIWLQRDFHIYVVNMFDTAKACEVLS-KPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLL 276
Cdd:COG0349   77 AAREDLEILYHLFGILPKPLFDTQIAAALLGyGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 277 YIADSLTTELKQLatdssspdDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL- 355
Cdd:COG0349  157 PLYEKLLEELERE--------GRLEWAEEECAR--LLDPATYREDPEE----------AWLRL-----KGAWKLNPRQLa 211

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 240254568 356 -VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEI 397
Cdd:COG0349  212 vLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEEL 254
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 127-309 1.84e-51

DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.


Pssm-ID: 176654 [Multi-domain]  Cd Length: 178  Bit Score: 178.11  E-value: 1.84e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 127 QLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGADNDVIWL 206
Cdd:cd06142    1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGD-LSPLKELLADPNIVKVFHAAREDLELL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 207 QRDFHIYVVNMFDTAKACEVLSKPQR-SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYIADSLTTE 285
Cdd:cd06142   80 KRDFGILPQNLFDTQIAARLLGLGDSvGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159

                        170       180
                 ....*....|....*....|....
gi 240254568 286 LKQLatdssspdDRFHFLLEASRR 309
Cdd:cd06142  160 LEEE--------GRLEWAEEECEL 175
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 140-282 3.24e-37

DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 176650 [Multi-domain]  Cd Length: 161  Bit Score: 137.26  E-value: 3.24e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 140 VFAVDTEQHSLRSFLGFTALIQISTHEE-DFLVDTIALHDVMSILRPVFSDPNICKVFHGADNDVIWLQRDFHIYVVNMF 218
Cdd:cd06129   15 VIAFDMEWPPGRRYYGEVALIQLCVSEEkCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLF 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 240254568 219 DTAKACEVLSKPQR-SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYIADSL 282
Cdd:cd06129   95 DTTIAANLKGLPERwSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 119-286 7.14e-35

3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes


Pssm-ID: 214681 [Multi-domain]  Cd Length: 172  Bit Score: 130.94  E-value: 7.14e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568   119 YVWVETESQLKELAEILAKEQ-VFAVDTEQHSLRSFLGFTALIQISTH-EEDFLVDTIALHDVMSILRPVFSDPNICKVF 196
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGgEVALDTETTGLDSYSGKLVLIQISVTgEGAFIIDPLALGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568   197 HGADNDVIWLQRdFHIYVVNMFDTAKACEVLSKPQR--SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSkhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 240254568   275 LLYIADSLTTEL 286
Cdd:smart00474 160 LLRLYEKLEKEL 171
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 121-452 1.51e-26

ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]


Pssm-ID: 130455 [Multi-domain]  Cd Length: 367  Bit Score: 112.56  E-value: 1.51e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGAD 200
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKVLHAAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  201 NDVIWLQRDFHIYVVNMFDTAKACEVLSKPQrSLAY--LLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYI 278
Cdd:TIGR01388  80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGM-SMGYakLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  279 ADSLTTELKQlatdssspDDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL--V 356
Cdd:TIGR01388 159 YAKLMERLEE--------SGRLAWLEEECTL--LTDRRTYVVNPED----------AWRDI-----KNAWQLRPQQLavL 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568  357 RKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEiydtiahidLATESSPSLSssvqspypvICSHLDDIYKMI 436
Cdd:TIGR01388 214 QALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTE---------LASLGPKGSE---------IRKHGDTLLALV 275

                         330
                  ....*....|....*.
gi 240254568  437 LDKLAKLDDLLPVVLK 452
Cdd:TIGR01388 276 KTALALPEDALPQAPL 291
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 122-277 8.37e-20

DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.


Pssm-ID: 176653 [Multi-domain]  Cd Length: 170  Bit Score: 87.63  E-value: 8.37e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 122 VETESQLKELAE-ILAKEQVFAVDTE-QHSLRSFL-GFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICKVFHG 198
Cdd:cd06141    1 TDSAQDAEEAVKeLLGKEKVVGFDTEwRPSFRKGKrNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVL--SKPQRSLAYLLETVCGVA--TNKLLQREDWRQRPLSEEMVRYARTDAH- 273
Cdd:cd06141   81 IKGDARKLARDFGIEVRGVVDLSHLAKRVgpRRKLVSLARLVEEVLGLPlsKPKKVRCSNWEARPLSKEQILYAATDAYa 160


                 ....*
gi 240254568 274 -YLLY 277
Cdd:cd06141  161 sLELY 165
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 121-282 1.95e-15

DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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.


Pssm-ID: 176655  Cd Length: 193  Bit Score: 75.41  E-value: 1.95e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 121 WVETESQLKELAE--ILAKEQVFAVDTE---QHSLRSFLGfTALIQISTHEEDFLVDTIALHDVMS-----ILRPVFSDP 190
Cdd:cd06146    3 IVDSEEELEALLLalSLEAGRVVGIDSEwkpSFLGDSDPR-VAILQLATEDEVFLLDLLALENLESedwdrLLKRLFEDP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 191 NICKVFHGADNDVIWLQRDF----------HIYV--------VNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQR 252
Cdd:cd06146   82 DVLKLGFGFKQDLKALSASYpalkcmfervQNVLdlqnlakeLQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQC 161

                        170       180       190
                 ....*....|....*....|....*....|
gi 240254568 253 EDWRQRPLSEEMVRYARTDAHYLLYIADSL 282
Cdd:cd06146  162 SNWERRPLREEQILYAALDAYCLLEVFDKL 191
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 140-278 3.15e-14

DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.


Pssm-ID: 176656 [Multi-domain]  Cd Length: 150  Bit Score: 70.73  E-value: 3.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 140 VFAVDTEQHSLRSFLGFTALIQISTHEED-FLVDTIALHDVMSILRPVFSDPNICKVFHGADNDVIWLQRDFHIYVVNMF 218
Cdd:cd09018    1 VFAFDTETDSLDNISANLVLIQLAIEPGVaALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 240254568 219 DTAKACEVLSKPQRS--LAYLLETVCGVATNKLLQRED--WRQRPLSEEMVRYARTDAHYLLYI 278
Cdd:cd09018   81 DTMLEAYILNSVAGRwdMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQI 144
PRK10829 PRK10829
ribonuclease D; Provisional
 119-288 2.08e-12

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 69.65  E-value: 2.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHG 198
Cdd:PRK10829   3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQVTKFLHA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRS-LAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLY 277
Cdd:PRK10829  82 GSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCgFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLP 161

                        170
                 ....*....|.
gi 240254568 278 IADSLTTELKQ 288
Cdd:PRK10829 162 IAAKLMAETEA 172
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 129-278 3.43e-10

DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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 conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.


Pssm-ID: 99851  Cd Length: 197  Bit Score: 60.38  E-value: 3.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 129 KELAEILAKEQVFAVDTEQHSLrSFLGFTALIQISTHEED-FLVDTIALhDVMSI---LRPVFSDPNICKVFHGADNDVI 204
Cdd:cd06148    1 KEAIIHLKKQKVIGLDCEGVNL-GRKGKLCLVQIATRTGQiYLFDILKL-GSIVFingLKDILESKKILKVIHDCRRDSD 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 205 WLQRDFHIYVVNMFDTAKA----CEVLSKP-----QRSLAYLLETVCGVATNKLLQ-----RED---WRQRPLSEEMVRY 267
Cdd:cd06148   79 ALYHQYGIKLNNVFDTQVAdallQEQETGGfnpdrVISLVQLLDKYLYISISLKEDvkklmREDpkfWALRPLTEDMIRY 158

                        170
                 ....*....|.
gi 240254568 268 ARTDAHYLLYI 278
Cdd:cd06148  159 AALDVLCLLPL 169
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 353-396 3.03e-07

HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.


Pssm-ID: 425755 [Multi-domain]  Cd Length: 68  Bit Score: 48.30  E-value: 3.03e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 240254568  353 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 396
Cdd:pfam00570   2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEE 45
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 351-398 1.12e-05

Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.


Pssm-ID: 128635 [Multi-domain]  Cd Length: 81  Bit Score: 44.21  E-value: 1.12e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 240254568   351 NAEELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEIY 398
Cdd:smart00341   3 RQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELL 50
PRK05755 PRK05755
DNA polymerase I; Provisional
 116-288 1.16e-05

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 49.32  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 116 SDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSF----LGFTalIQISTHEEDFLVDTIALHDVMSILRPVFSDPN 191
Cdd:PRK05755 293 EEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMqaelVGLS--FAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 192 ICKVFHGADNDVIWLQRdFHIYVVNM-FDTAKAcevlskpqrslAYLLETVCGVATNKLLQREDWRQRPLSEEMV----- 265
Cdd:PRK05755 371 IKKVGQNLKYDLHVLAR-YGIELRGIaFDTMLA-----------SYLLDPGRRHGLDSLAERYLGHKTISFEEVAgkqlt 438

                        170       180       190
                 ....*....|....*....|....*....|...
gi 240254568 266 ----------RYARTDAHYLLYIADSLTTELKQ 288
Cdd:PRK05755 439 faqvdleeaaEYAAEDADVTLRLHEVLKPKLLE 471
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 135-288 6.47e-03

DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.


Pssm-ID: 176651 [Multi-domain]  Cd Length: 193  Bit Score: 38.66  E-value: 6.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 135 LAKEQVFAVDTEQHSLRSFLGFTALIQISTHEE---------DFLVDTIALHDVMSILRPVFSDPNICKVFHGA--DNDV 203
Cdd:cd06139    2 LEKAKVFAFDTETTSLDPMQAELVGISFAVEPGeayyiplghDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLkfDLHV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240254568 204 IwlqRDFHIYVVNM-FDTAKACEVL--SKPQRSLAYL-----------LETVCGVATNKLlqreDWRQRPLsEEMVRYAR 269
Cdd:cd06139   82 L---ANHGIELRGPaFDTMLASYLLnpGRRRHGLDDLaerylghktisFEDLVGKGKKQI----TFDQVPL-EKAAEYAA 153

                        170
                 ....*....|....*....
gi 240254568 270 TDAHYLLYIADSLTTELKQ 288
Cdd:cd06139  154 EDADITLRLYELLKPKLKE 172
 
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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