NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1063705540|ref|NP_001323729|]
View 

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 115-309 5.07e-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: 314.92  E-value: 5.07e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147     1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147    81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063705540 275 LLYIADSLTTELKQLateDSSSPDDRFHFLLEASR 309
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 ...
 354-397 3.09e-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: 3.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063705540 354 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 397
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 ...
 115-309 5.07e-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: 314.92  E-value: 5.07e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147     1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147    81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063705540 275 LLYIADSLTTELKQLateDSSSPDDRFHFLLEASR 309
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 7.96e-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: 7.96e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLR--SFLGFTALIQISTHEEDFLVDTIALHD-VMSILRPVFSDPNICKV 195
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDdVLSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 196 FHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQ-RSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
gi 1063705540 275 LLYIADSLTTELK 287
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
121-398 6.61e-52

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 185.85  E-value: 6.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSF---LGftaLIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFH 197
Cdd:COG0349     1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYyprLC---LIQLADGEEVALIDPLAIGD-LSPLWELLADPAIVKVFH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 198 GADNDVIWLQRDFHIYVVNMFDTAKACEVLS-KPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLL 276
Cdd:COG0349    77 AAREDLEILYHLFGILPKPLFDTQIAAALLGyGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 277 YIADSLTTELKQLatedssspdDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL 356
Cdd:COG0349   157 PLYEKLLEELERE---------GRLEWAEEECAR--LLDPATYREDPEE----------AWLRL-----KGAWKLNPRQL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1063705540 357 --VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEI 398
Cdd:COG0349   211 avLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEEL 254
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 119-286 7.29e-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: 7.29e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540  119 YVWVETESQLKELAEILAKEQ-VFAVDTEQHSLRSFLGFTALIQISTH-EEDFLVDTIALHDVMSILRPVFSDPNICKVF 196
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGgEVALDTETTGLDSYSGKLVLIQISVTgEGAFIIDPLALGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540  197 HGADNDVIWLQRdFHIYVVNMFDTAKACEVLSKPQR--SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSkhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 1063705540  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 ...
 121-453 2.02e-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: 112.17  E-value: 2.02e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGAD 200
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKVLHAAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 201 NDVIWLQRDFHIYVVNMFDTAKACEVLSKPQrSLAY--LLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYI 278
Cdd:TIGR01388  80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGM-SMGYakLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 279 ADSLTTELKQlatedssspDDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL-- 356
Cdd:TIGR01388 159 YAKLMERLEE---------SGRLAWLEEECTL--LTDRRTYVVNPED----------AWRDI-----KNAWQLRPQQLav 212

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 357 VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEiydtiahidLATESSPSLSssvqspypvICSHLDDIYKM 436
Cdd:TIGR01388 213 LQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTE---------LASLGPKGSE---------IRKHGDTLLAL 274

                         330
                  ....*....|....*..
gi 1063705540 437 ILDKLAKLDDLLPVVLK 453
Cdd:TIGR01388 275 VKTALALPEDALPQAPL 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 1063705540 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHG 198
Cdd:PRK10829    3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQVTKFLHA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRS-LAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLY 277
Cdd:PRK10829   82 GSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCgFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLP 161

                         170
                  ....*....|.
gi 1063705540 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 ...
 354-397 3.09e-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: 3.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063705540 354 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 397
Cdd:pfam00570   2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEE 45
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 352-399 1.15e-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: 1.15e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1063705540  352 NAEELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEIY 399
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 ...
 115-309 5.07e-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: 314.92  E-value: 5.07e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 115 MSDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICK 194
Cdd:cd06147     1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 195 VFHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:cd06147    81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1063705540 275 LLYIADSLTTELKQLateDSSSPDDRFHFLLEASR 309
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 7.96e-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: 7.96e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLR--SFLGFTALIQISTHEEDFLVDTIALHD-VMSILRPVFSDPNICKV 195
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDdVLSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 196 FHGADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQ-RSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
gi 1063705540 275 LLYIADSLTTELK 287
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
121-398 6.61e-52

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 185.85  E-value: 6.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSF---LGftaLIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFH 197
Cdd:COG0349     1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYyprLC---LIQLADGEEVALIDPLAIGD-LSPLWELLADPAIVKVFH 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 198 GADNDVIWLQRDFHIYVVNMFDTAKACEVLS-KPQRSLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLL 276
Cdd:COG0349    77 AAREDLEILYHLFGILPKPLFDTQIAAALLGyGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 277 YIADSLTTELKQLatedssspdDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL 356
Cdd:COG0349   157 PLYEKLLEELERE---------GRLEWAEEECAR--LLDPATYREDPEE----------AWLRL-----KGAWKLNPRQL 210

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1063705540 357 --VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEI 398
Cdd:COG0349   211 avLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEEL 254
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 127-310 2.56e-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: 177.73  E-value: 2.56e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 127 QLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGADNDVIWL 206
Cdd:cd06142     1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGD-LSPLKELLADPNIVKVFHAAREDLELL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 207 QRDFHIYVVNMFDTAKACEVLSKPQR-SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYIADSLTTE 285
Cdd:cd06142    80 KRDFGILPQNLFDTQIAARLLGLGDSvGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159

                         170       180
                  ....*....|....*....|....*
gi 1063705540 286 LKQLatedssspdDRFHFLLEASRR 310
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 3.21e-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: 3.21e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 140 VFAVDTEQHSLRSFLGFTALIQISTHEE-DFLVDTIALHDVMSILRPVFSDPNICKVFHGADNDVIWLQRDFHIYVVNMF 218
Cdd:cd06129    15 VIAFDMEWPPGRRYYGEVALIQLCVSEEkCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLF 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063705540 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 7.29e-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: 7.29e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540  119 YVWVETESQLKELAEILAKEQ-VFAVDTEQHSLRSFLGFTALIQISTH-EEDFLVDTIALHDVMSILRPVFSDPNICKVF 196
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGgEVALDTETTGLDSYSGKLVLIQISVTgEGAFIIDPLALGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540  197 HGADNDVIWLQRdFHIYVVNMFDTAKACEVLSKPQR--SLAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHY 274
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSkhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 1063705540  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 ...
 121-453 2.02e-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: 112.17  E-value: 2.02e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 121 WVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHGAD 200
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIID-WSPLKELLRDESVVKVLHAAS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 201 NDVIWLQRDFHIYVVNMFDTAKACEVLSKPQrSLAY--LLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLYI 278
Cdd:TIGR01388  80 EDLEVFLNLFGELPQPLFDTQIAAAFCGFGM-SMGYakLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPL 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 279 ADSLTTELKQlatedssspDDRFHFLLEASRRsnMTCLQLYTKETEDfpgsaasssiIYRHLnghgdKSNISLNAEEL-- 356
Cdd:TIGR01388 159 YAKLMERLEE---------SGRLAWLEEECTL--LTDRRTYVVNPED----------AWRDI-----KNAWQLRPQQLav 212

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 357 VRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEiydtiahidLATESSPSLSssvqspypvICSHLDDIYKM 436
Cdd:TIGR01388 213 LQALAAWREREARERDLPRNFVLKEEALWELARQAPGNLTE---------LASLGPKGSE---------IRKHGDTLLAL 274

                         330
                  ....*....|....*..
gi 1063705540 437 ILDKLAKLDDLLPVVLK 453
Cdd:TIGR01388 275 VKTALALPEDALPQAPL 291
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 122-277 7.98e-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: 7.98e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 122 VETESQLKELAE-ILAKEQVFAVDTE-QHSLRSFL-GFTALIQISTHEEDFLVDTIALHDVMSILRPVFSDPNICKVFHG 198
Cdd:cd06141     1 TDSAQDAEEAVKeLLGKEKVVGFDTEwRPSFRKGKrNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVL--SKPQRSLAYLLETVCGVA--TNKLLQREDWRQRPLSEEMVRYARTDAH- 273
Cdd:cd06141    81 IKGDARKLARDFGIEVRGVVDLSHLAKRVgpRRKLVSLARLVEEVLGLPlsKPKKVRCSNWEARPLSKEQILYAATDAYa 160


                  ....*
gi 1063705540 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 1.96e-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: 1.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 121 WVETESQLKELAE--ILAKEQVFAVDTE---QHSLRSFLGfTALIQISTHEEDFLVDTIALHDVMS-----ILRPVFSDP 190
Cdd:cd06146     3 IVDSEEELEALLLalSLEAGRVVGIDSEwkpSFLGDSDPR-VAILQLATEDEVFLLDLLALENLESedwdrLLKRLFEDP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 191 NICKVFHGADNDVIWLQRDF----------HIYV--------VNMFDTAKACEVLSKPQRSLAYLLETVCGVATNKLLQR 252
Cdd:cd06146    82 DVLKLGFGFKQDLKALSASYpalkcmfervQNVLdlqnlakeLQKSDMGRLKGNLPSKTKGLADLVQEVLGKPLDKSEQC 161

                         170       180       190
                  ....*....|....*....|....*....|
gi 1063705540 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 3.31e-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: 3.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 140 VFAVDTEQHSLRSFLGFTALIQISTHEED-FLVDTIALHDVMSILRPVFSDPNICKVFHGADNDVIWLQRDFHIYVVNMF 218
Cdd:cd09018     1 VFAFDTETDSLDNISANLVLIQLAIEPGVaALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063705540 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 1063705540 119 YVWVETESQLKELAEILAKEQVFAVDTEQHSLRSFLGFTALIQISTHEEDFLVDTIALHDvMSILRPVFSDPNICKVFHG 198
Cdd:PRK10829    3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITD-WSPFKALLRDPQVTKFLHA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 199 ADNDVIWLQRDFHIYVVNMFDTAKACEVLSKPQRS-LAYLLETVCGVATNKLLQREDWRQRPLSEEMVRYARTDAHYLLY 277
Cdd:PRK10829   82 GSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCgFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLP 161

                         170
                  ....*....|.
gi 1063705540 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 ...
 129-296 3.07e-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: 3.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 129 KELAEILAKEQVFAVDTEQHSLrSFLGFTALIQISTHEED-FLVDTIALhDVMSI---LRPVFSDPNICKVFHGADNDVI 204
Cdd:cd06148     1 KEAIIHLKKQKVIGLDCEGVNL-GRKGKLCLVQIATRTGQiYLFDILKL-GSIVFingLKDILESKKILKVIHDCRRDSD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 205 WLQRDFHIYVVNMFDTAKA----CEVLSKP-----QRSLAYLLETVCGVATNKLLQ-----RED---WRQRPLSEEMVRY 267
Cdd:cd06148    79 ALYHQYGIKLNNVFDTQVAdallQEQETGGfnpdrVISLVQLLDKYLYISISLKEDvkklmREDpkfWALRPLTEDMIRY 158

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1063705540 268 ARTDAHYLLY---------IADSLTTELKQLATEDSSS 296
Cdd:cd06148   159 AALDVLCLLPlyyamldalISKFLKAVFKYLNTERNLS 196
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 354-397 3.09e-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: 3.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063705540 354 EELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEE 397
Cdd:pfam00570   2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEE 45
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 352-399 1.15e-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: 1.15e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1063705540  352 NAEELVRKLCAWRDLMGRIHDESTRYVLSDQAIVGLSCKQPTTTEEIY 399
Cdd:smart00341   3 RQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELL 50
PRK05755 PRK05755
DNA polymerase I; Provisional
 116-288 1.17e-05

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 49.32  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 116 SDSYVWVETESQLKELAEILAKEQVFAVDTEQHSLRSF----LGFTalIQISTHEEDFLVDTIALHDVMSILRPVFSDPN 191
Cdd:PRK05755  293 EEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLDPMqaelVGLS--FAVEPGEAAYIPLDQLDREVLAALKPLLEDPA 370

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 192 ICKVFHGADNDVIWLQRdFHIYVVNM-FDTAKAcevlskpqrslAYLLETVCGVATNKLLQREDWRQRPLSEEMV----- 265
Cdd:PRK05755  371 IKKVGQNLKYDLHVLAR-YGIELRGIaFDTMLA-----------SYLLDPGRRHGLDSLAERYLGHKTISFEEVAgkqlt 438

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1063705540 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 6.66e-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: 6.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 135 LAKEQVFAVDTEQHSLRSFLGFTALIQISTHEE---------DFLVDTIALHDVMSILRPVFSDPNICKVFHGA--DNDV 203
Cdd:cd06139     2 LEKAKVFAFDTETTSLDPMQAELVGISFAVEPGeayyiplghDYGGEQLPREEVLAALKPLLEDPSIKKVGQNLkfDLHV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063705540 204 IwlqRDFHIYVVNM-FDTAKACEVL--SKPQRSLAYL-----------LETVCGVATNKLlqreDWRQRPLsEEMVRYAR 269
Cdd:cd06139    82 L---ANHGIELRGPaFDTMLASYLLnpGRRRHGLDDLaerylghktisFEDLVGKGKKQI----TFDQVPL-EKAAEYAA 153

                         170
                  ....*....|....*....
gi 1063705540 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH