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Conserved domains on  [gi|15596491|ref|NP_249985|]
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ribonuclease D [Pseudomonas aeruginosa PAO1]

Protein Classification

ribonuclease D( domain architecture ID 11492394)

ribonuclease D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA by catalyzing the exonucleolytic cleavage of extra residues from the 3'-terminus of tRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 8-374 0e+00

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: 513.16  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     8 WIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSE 87
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    88 DLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYL 167
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   168 ALDTRLSEEKRAWLLEDGAELVANL-CRESDPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVLRERTL 246
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRrTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   247 WPLARLLPKNKTDLAAIEdMHPRTVRQDGDFLIELIAQAARLPQSEW-PEALPEPLPPEVTPLLKSLRAIGQREAETLGM 325
Cdd:TIGR01388 241 WELARQAPGNLTELASLG-PKGSEIRKHGDTLLALVKTALALPEDALpQAPLNLMPPPGYKALFKLLKVLVKDVSETLGL 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 15596491   326 APELMLRKKVLEALLKSGYPDGPYELPDSLRGWRRErMGQALLDALESA 374
Cdd:TIGR01388 320 ASELLASRRQLEQLLAWGWKLKPNALPPLLQGWRRE-LGEEALKNLLSE 367
 
Name Accession Description Interval E-value
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 8-374 0e+00

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: 513.16  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     8 WIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSE 87
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    88 DLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYL 167
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   168 ALDTRLSEEKRAWLLEDGAELVANL-CRESDPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVLRERTL 246
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRrTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   247 WPLARLLPKNKTDLAAIEdMHPRTVRQDGDFLIELIAQAARLPQSEW-PEALPEPLPPEVTPLLKSLRAIGQREAETLGM 325
Cdd:TIGR01388 241 WELARQAPGNLTELASLG-PKGSEIRKHGDTLLALVKTALALPEDALpQAPLNLMPPPGYKALFKLLKVLVKDVSETLGL 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 15596491   326 APELMLRKKVLEALLKSGYPDGPYELPDSLRGWRRErMGQALLDALESA 374
Cdd:TIGR01388 320 ASELLASRRQLEQLLAWGWKLKPNALPPLLQGWRRE-LGEEALKNLLSE 367
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
8-372 1.13e-147

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 421.97  E-value: 1.13e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   8 WIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSE 87
Cdd:COG0349   1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  88 DLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYL 167
Cdd:COG0349  81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491 168 ALDTRLSEEKR-AWLLEDGAELVANLCRESDPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVLRERTL 246
Cdd:COG0349 161 KLLEELEREGRlEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491 247 WPLARLLPKNKTDLAAIEDMHPRTVRQDGDFLIELIAQAARLPQSEW-PEALPEPLPPEVTPLLKSLRAIGQREAETLGM 325
Cdd:COG0349 241 LELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALPEEELpEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320

                       330       340       350       360
                ....*....|....*....|....*....|....*....|....*..
gi 15596491 326 APELMLRKKVLEALLKsgypDGPYELPDSLRGWRRERMGQALLDALE 372
Cdd:COG0349 321 APELLASRKDLEALAR----WGELADPPLLSGWRRELFGEELLALLE 363
PRK10829 PRK10829
ribonuclease D; Provisional
 7-372 2.10e-88

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 271.11  E-value: 2.10e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    7 QWIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACS 86
Cdd:PRK10829   4 QMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   87 EDLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLaqvy 166
Cdd:PRK10829  84 EDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYL---- 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  167 LALDTRLSEEKRA--WL--LEDGAELVANLCRES-DPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVL 241
Cdd:PRK10829 160 LPIAAKLMAETEAagWLpaALDECRLLCQRRQEVlAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVV 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  242 RERTLWPLARLLPKNKTDLAAIeDMHPRTVRQDGDFLIELIAQAARLPQSEwpealpepLPPEVTPLL---------KSL 312
Cdd:PRK10829 240 REEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEA--------LPPPVLNLIdmpgyrkafKAI 310

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596491  313 RAIGQREAETLGMAPELMLRKKVLEALLKSGYPDGPYE-LPDSLRGWRRERMGQALLDALE 372
Cdd:PRK10829 311 KALIQEVSETHGLSAELLASRRQINQLLNWHWKLKPQNgLPELISGWRGELLAEALTEILQ 371
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 14-190 1.41e-72

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: 223.95  E-value: 1.41e-72
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  14 SLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSEDLEVFL 93
Cdd:cd06142   1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  94 RLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYLALDTRL 173
Cdd:cd06142  81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160

                       170
                ....*....|....*...
gi 15596491 174 SEEKR-AWLLEDGAELVA 190
Cdd:cd06142 161 EEEGRlEWAEEECELLLD 178
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 6-173 4.38e-41

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: 142.44  E-value: 4.38e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     6 IQWIRDDASLAQQCREWRTQPYLALDTEFMRVDT--FYPAAGLVQVGDGRQEWLIDPLLIQDW--SPFAELLEDERVVKV 81
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTysYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    82 LHACSEDLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQH 161
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|..
gi 15596491   162 LAQVYLALDTRL 173
Cdd:pfam01612 161 LLRLYDKLRKEL 172
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 6-173 6.33e-27

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: 105.13  E-value: 6.33e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491      6 IQWIRDDASLAQQC-REWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQE-WLIDPLLIQD-WSPFAELLEDERVVKVL 82
Cdd:smart00474   1 VIVVTDSETLEELLeKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGaFIIDPLALGDdLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     83 HACSEDLEVFLRLtGSLPVPLFDTQLAAAYLGMAHSM-GYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQH 161
Cdd:smart00474  81 HNAKFDLHVLARF-GIELENIFDTMLAAYLLLGGPSKhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 15596491    162 LAQVYLALDTRL 173
Cdd:smart00474 160 LLRLYEKLEKEL 171
 
Name Accession Description Interval E-value
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 8-374 0e+00

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: 513.16  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     8 WIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSE 87
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    88 DLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYL 167
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   168 ALDTRLSEEKRAWLLEDGAELVANL-CRESDPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVLRERTL 246
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRrTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   247 WPLARLLPKNKTDLAAIEdMHPRTVRQDGDFLIELIAQAARLPQSEW-PEALPEPLPPEVTPLLKSLRAIGQREAETLGM 325
Cdd:TIGR01388 241 WELARQAPGNLTELASLG-PKGSEIRKHGDTLLALVKTALALPEDALpQAPLNLMPPPGYKALFKLLKVLVKDVSETLGL 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 15596491   326 APELMLRKKVLEALLKSGYPDGPYELPDSLRGWRRErMGQALLDALESA 374
Cdd:TIGR01388 320 ASELLASRRQLEQLLAWGWKLKPNALPPLLQGWRRE-LGEEALKNLLSE 367
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
8-372 1.13e-147

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 421.97  E-value: 1.13e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   8 WIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSE 87
Cdd:COG0349   1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  88 DLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYL 167
Cdd:COG0349  81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491 168 ALDTRLSEEKR-AWLLEDGAELVANLCRESDPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVLRERTL 246
Cdd:COG0349 161 KLLEELEREGRlEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491 247 WPLARLLPKNKTDLAAIEDMHPRTVRQDGDFLIELIAQAARLPQSEW-PEALPEPLPPEVTPLLKSLRAIGQREAETLGM 325
Cdd:COG0349 241 LELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALPEEELpEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320

                       330       340       350       360
                ....*....|....*....|....*....|....*....|....*..
gi 15596491 326 APELMLRKKVLEALLKsgypDGPYELPDSLRGWRRERMGQALLDALE 372
Cdd:COG0349 321 APELLASRKDLEALAR----WGELADPPLLSGWRRELFGEELLALLE 363
PRK10829 PRK10829
ribonuclease D; Provisional
 7-372 2.10e-88

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 271.11  E-value: 2.10e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    7 QWIRDDASLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACS 86
Cdd:PRK10829   4 QMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   87 EDLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLaqvy 166
Cdd:PRK10829  84 EDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYL---- 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  167 LALDTRLSEEKRA--WL--LEDGAELVANLCRES-DPREAYREVKLGWRLRPQQLAVLRELCAWREEQARLRNRPRNHVL 241
Cdd:PRK10829 160 LPIAAKLMAETEAagWLpaALDECRLLCQRRQEVlAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVV 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  242 RERTLWPLARLLPKNKTDLAAIeDMHPRTVRQDGDFLIELIAQAARLPQSEwpealpepLPPEVTPLL---------KSL 312
Cdd:PRK10829 240 REEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEA--------LPPPVLNLIdmpgyrkafKAI 310

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15596491  313 RAIGQREAETLGMAPELMLRKKVLEALLKSGYPDGPYE-LPDSLRGWRRERMGQALLDALE 372
Cdd:PRK10829 311 KALIQEVSETHGLSAELLASRRQINQLLNWHWKLKPQNgLPELISGWRGELLAEALTEILQ 371
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 14-190 1.41e-72

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: 223.95  E-value: 1.41e-72
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  14 SLAQQCREWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLIQDWSPFAELLEDERVVKVLHACSEDLEVFL 93
Cdd:cd06142   1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  94 RLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYLALDTRL 173
Cdd:cd06142  81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160

                       170
                ....*....|....*...
gi 15596491 174 SEEKR-AWLLEDGAELVA 190
Cdd:cd06142 161 EEEGRlEWAEEECELLLD 178
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 6-173 4.38e-41

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: 142.44  E-value: 4.38e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     6 IQWIRDDASLAQQCREWRTQPYLALDTEFMRVDT--FYPAAGLVQVGDGRQEWLIDPLLIQDW--SPFAELLEDERVVKV 81
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTysYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    82 LHACSEDLEVFLRLTGSLPVPLFDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQH 161
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|..
gi 15596491   162 LAQVYLALDTRL 173
Cdd:pfam01612 161 LLRLYDKLRKEL 172
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 26-166 1.61e-32

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: 119.54  E-value: 1.61e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  26 PYLALDTEFMRVDTFYPAAGLVQVGDGRQE-WLIDPL-LIQDWSPFAELLEDERVVKVLHACSEDLEVFLRLTGSLPVPL 103
Cdd:cd06129  14 DVIAFDMEWPPGRRYYGEVALIQLCVSEEKcYLFDPLsLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRL 93

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15596491 104 FDTQLAAAYLGMAHSMGYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVY 166
Cdd:cd06129  94 FDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIY 156
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 28-169 8.62e-28

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: 106.55  E-value: 8.62e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  28 LALDTEFMRVDTFYPAAGLVQVGDGRQE-WLIDPLLIQ-DWSPFAELLEDERVVKVLHACSEDLEVFLRLTGSLPVPLFD 105
Cdd:cd09018   2 FAFDTETDSLDNISANLVLIQLAIEPGVaALIPVAHDYlALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFD 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596491 106 TQLAAAYLG-MAHSMGYSKLVKEVLDIDLPKDETRSD--WLQRPLTEMQMRYAADDVQHLAQVYLAL 169
Cdd:cd09018  82 TMLEAYILNsVAGRWDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 6-173 6.33e-27

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: 105.13  E-value: 6.33e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491      6 IQWIRDDASLAQQC-REWRTQPYLALDTEFMRVDTFYPAAGLVQVGDGRQE-WLIDPLLIQD-WSPFAELLEDERVVKVL 82
Cdd:smart00474   1 VIVVTDSETLEELLeKLRAAGGEVALDTETTGLDSYSGKLVLIQISVTGEGaFIIDPLALGDdLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491     83 HACSEDLEVFLRLtGSLPVPLFDTQLAAAYLGMAHSM-GYSKLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQH 161
Cdd:smart00474  81 HNAKFDLHVLARF-GIELENIFDTMLAAYLLLGGPSKhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|..
gi 15596491    162 LAQVYLALDTRL 173
Cdd:smart00474 160 LLRLYEKLEKEL 171
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 16-169 4.65e-16

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: 74.92  E-value: 4.65e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  16 AQQCREW-----RTQPYLALDTEFmrVDTFYPAA----GLVQVGDGRQEWLIDPLLIQDWSP-FAELLEDERVVKVLHAC 85
Cdd:cd06141   4 AQDAEEAvkellGKEKVVGFDTEW--RPSFRKGKrnkvALLQLATESRCLLFQLAHMDKLPPsLKQLLEDPSILKVGVGI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  86 SEDLEVFLRLTGSLPVPLFDTQ-LAAAYLGMAHSMGYSKLVKEVL--DIDLPKDETRSDWLQRPLTEMQMRYAADDVQHL 162
Cdd:cd06141  82 KGDARKLARDFGIEVRGVVDLShLAKRVGPRRKLVSLARLVEEVLglPLSKPKKVRCSNWEARPLSKEQILYAATDAYAS 161


                ....*..
gi 15596491 163 AQVYLAL 169
Cdd:cd06141 162 LELYRKL 168
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 215-282 3.42e-15

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: 69.49  E-value: 3.42e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596491   215 QLAVLRELCAWREEQARLRNRPRNHVLRERTLWPLARLLPKNKTDLAAIEDMHPRTVRQDGDFLIELI 282
Cdd:pfam00570   1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEEILAAI 68
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 6-169 1.47e-14

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: 71.56  E-value: 1.47e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   6 IQWIRDDASLAQQCREW--RTQPYLALDTEFM--RVDTFYPAAGLVQVGDGRQEWLID-----PLLIQDWSPFA-ELLED 75
Cdd:cd06146   1 IHIVDSEEELEALLLALslEAGRVVGIDSEWKpsFLGDSDPRVAILQLATEDEVFLLDllaleNLESEDWDRLLkRLFED 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  76 ERVVKVLHACSEDLEVfLRLTGSLPVPLF-------DTQLAAAYLgMAHSM------------GYSKLVKEVLDIDLPKD 136
Cdd:cd06146  81 PDVLKLGFGFKQDLKA-LSASYPALKCMFervqnvlDLQNLAKEL-QKSDMgrlkgnlpsktkGLADLVQEVLGKPLDKS 158

                       170       180       190
                ....*....|....*....|....*....|...
gi 15596491 137 ETRSDWLQRPLTEMQMRYAADDVQHLAQVYLAL 169
Cdd:cd06146 159 EQCSNWERRPLREEQILYAALDAYCLLEVFDKL 191
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 17-173 3.90e-13

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: 67.24  E-value: 3.90e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  17 QQCREwrtqpyLALDTEFMRVDTFYPAAGLVQVGDGRQEWLIDPLLI-QDWSPFAELLEDERVVKVLHACSEDLEVFLRL 95
Cdd:cd06147  22 KNCKE------IAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLrDDMHILNEVFTDPNILKVFHGADSDIIWLQRD 95

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15596491  96 TGSLPVPLFDTQLAAAYLGMA-HSMGYskLVKEVLDIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYLALDTRL 173
Cdd:cd06147  96 FGLYVVNLFDTGQAARVLNLPrHSLAY--LLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNEL 172
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 212-289 3.09e-10

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: 56.15  E-value: 3.09e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15596491    212 RPQQLAVLRELCAWREEQARLRNRPRNHVLRERTLWPLARLLPKNKTDLAAIEDMHPRTVRQDGDFLIELIAQAARLP 289
Cdd:smart00341   1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSP 78
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 69-179 3.80e-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: 58.84  E-value: 3.80e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  69 FAELLEDERVVKVLHACSEDLEVflrLTGSLPVPL---FDTQLAAAYLGMAHSMGYSK----------------LVKEVL 129
Cdd:cd06148  57 LKDILESKKILKVIHDCRRDSDA---LYHQYGIKLnnvFDTQVADALLQEQETGGFNPdrvislvqlldkylyiSISLKE 133

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 15596491 130 DIDLPKDETRSDWLQRPLTEMQMRYAADDVQHLAQVYLA-LDTRLSEEKRA 179
Cdd:cd06148 134 DVKKLMREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAmLDALISKFLKA 184
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 25-184 1.89e-08

DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 55.83  E-value: 1.89e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  25 QPYLALDTEFMRVDtfYPAAGLVQVG----DGR---------QEWLIDplLIQDWSPFAELLEDERVVKVLHACSEDLEV 91
Cdd:COG0749   1 AGLVAFDTETTSLD--PMDAELVGISfavePGEaayiplahgAPEQLD--LDEVLAALKPLLEDPAIPKIGQNLKYDLHV 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  92 FLRLTGSLPVPLFDTQLaAAYL----GMAHSMGYskLVKEVLDIDLPKDE-------TRSDWLQRPLtEMQMRYAADDVQ 160
Cdd:COG0749  77 LARYGIELAGVAFDTML-ASYLlnpgRRRHGLDD--LAERYLGHETISYEelagkgkKQLTFDQVPL-EEAAEYAAEDAD 152

                       170       180
                ....*....|....*....|....
gi 15596491 161 HLAQVYLALDTRLSEEKRAWLLED 184
Cdd:COG0749 153 ITLRLHEVLKPELEEEGLLKLYEE 176
PRK05755 PRK05755
DNA polymerase I; Provisional
 2-184 2.12e-08

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 55.87  E-value: 2.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491    2 TAPEIQWIRDDASLAQQCREWRTQPYLALDTEFMRVDtfYPAAGLV----QVGDGRQEWL-IDPLLIQDWSPFAELLEDE 76
Cdd:PRK05755 292 DEEDYETILDEEELEAWLAKLKAAGLFAFDTETTSLD--PMQAELVglsfAVEPGEAAYIpLDQLDREVLAALKPLLEDP 369

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   77 RVVKVLHACSEDLEVFLRLTGSLPVPLFDTQLaAAYL---GMAHSMgySKLVKEVLDIDLP-------KDETRSDWLQRP 146
Cdd:PRK05755 370 AIKKVGQNLKYDLHVLARYGIELRGIAFDTML-ASYLldpGRRHGL--DSLAERYLGHKTIsfeevagKQLTFAQVDLEE 446

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 15596491  147 LTEmqmrYAADDVQHLAQVYLALDTRLSEEKR-AWLLED 184
Cdd:PRK05755 447 AAE----YAAEDADVTLRLHEVLKPKLLEEPGlLELYEE 481
DNA_polA_I_Bacillus_like_exo cd06140
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ...
 49-184 2.93e-06

inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.


Pssm-ID: 176652 [Multi-domain]  Cd Length: 178  Bit Score: 47.26  E-value: 2.93e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  49 VGDGRQEWLID-PLLIQDWSPFAELLEDERVVKVLHACSEDLEVFLRLTGSLPVPLFDTQLaAAYL--GMAHSMGYSKLV 125
Cdd:cd06140  27 LANGGGAYYIPlELALLDLAALKEWLEDEKIPKVGHDAKRAYVALKRHGIELAGVAFDTML-AAYLldPTRSSYDLADLA 105

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15596491 126 KEVLDIDLPKDETRSDWLQR---PLTEMQMRYAADDVQHLAQVYLALDTRLSEEKRAWLLED 184
Cdd:cd06140 106 KRYLGRELPSDEEVYGKGAKfavPDEEVLAEHLARKAAAIARLAPKLEEELEENEQLELYYE 167
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 69-182 3.80e-06

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: 47.13  E-value: 3.80e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  69 FAELLEDERVVKVLHACSEDLEVFLRLTGSLPVPLFDTQLaAAYL----GMAHSMgySKLVKEVLDIDLP-------KDE 137
Cdd:cd06139  59 LKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTML-ASYLlnpgRRRHGL--DDLAERYLGHKTIsfedlvgKGK 135

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 15596491 138 TRSDWLQRPLTEMqMRYAADDVQHLAQVYLALDTRLSEEKRAWLL 182
Cdd:cd06139 136 KQITFDQVPLEKA-AEYAAEDADITLRLYELLKPKLKEEPGLLEL 179
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 29-112 2.28e-04

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which 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 patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


Pssm-ID: 176647 [Multi-domain]  Cd Length: 96  Bit Score: 39.73  E-value: 2.28e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491  29 ALDTEFMRVDTFYPAAGLVQVGDGRqewlIDPLLIQDWSPFaeLLEDERVVKVLHACSEDLEVF----LRLTGS---LPV 101
Cdd:cd06125   2 AIDTEATGLDGAVHEIIEIALADVN----PEDTAVIDLKDI--LRDKPLAILVGHNGSFDLPFLnnrcAELGLKyplLAG 75

                        90
                ....*....|.
gi 15596491 102 PLFDTQLAAAY 112
Cdd:cd06125  76 SWIDTIKLAAD 86
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 26-179 6.60e-04

bifunctional 3'-5' exonuclease/DNA polymerase; Provisional


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 41.51  E-value: 6.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15596491   26 PYLALDTEFMRVDtfyPAAGLVQVGDGRQEWLIDPLliqdwspfaelledERVVKVLHACSEDLEvflrltgslpvPLFD 105
Cdd:PRK14975  23 GVVAGDTETTGDD---AAAAAAQEGEEEPRWVWAST--------------AALYPRLLAAGVRVE-----------RCHD 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15596491  106 TQLAAAYLGM---AHSMGYSKLVKEVLDIDLPKDETRSDWLqRPLTEMQMRYAADDVQHLAQVYLALDTRLSEEKRA 179
Cdd:PRK14975  75 LMLASQLLLGsegRAGSSLSAAAARALGEGLDKPPQTSALS-DPPDEEQLLYAAADADVLLELYAVLADQLNRIAAA 150
 
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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