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Conserved domains on  [gi|75765643|pdb|1YT3|A]
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Chain A, Ribonuclease D

Protein Classification

ribonuclease D( domain architecture ID 11484973)

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
PRK10829 PRK10829
ribonuclease D; Provisional
 1-373 0e+00

ribonuclease D; Provisional


:

Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 805.38  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLH 80
Cdd:PRK10829   1 MNYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        81 AGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLL 160
Cdd:PRK10829  81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       161 PITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
Cdd:PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       241 EEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSET 320
Cdd:PRK10829 241 EEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAFKAIKALIQEVSET 320

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
1YT3_A       321 HKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALHNLLQEY 373
Cdd:PRK10829 321 HGLSAELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLAEALTEILQEY 373
 
Name Accession Description Interval E-value
PRK10829 PRK10829
ribonuclease D; Provisional
 1-373 0e+00

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 805.38  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLH 80
Cdd:PRK10829   1 MNYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        81 AGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLL 160
Cdd:PRK10829  81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       161 PITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
Cdd:PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       241 EEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSET 320
Cdd:PRK10829 241 EEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAFKAIKALIQEVSET 320

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
1YT3_A       321 HKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALHNLLQEY 373
Cdd:PRK10829 321 HGLSAELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLAEALTEILQEY 373
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 5-372 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: 585.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          5 MITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSE 84
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         85 DLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITA 164
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        165 KLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        245 WSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKIS 324
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
1YT3_A        325 AELLASRRQINQLLNWHWKLKPqNNLPELISGWRGELMAEALHNLLQE 372
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKP-NALPPLLQGWRRELGEEALKNLLSE 367
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
5-373 2.94e-171

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 481.68  E-value: 2.94e-171
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        5 MITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSE 84
Cdd:COG0349   1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       85 DLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITA 164
Cdd:COG0349  81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A      165 KLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A      245 WSVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKI 323
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|
1YT3_A      324 SAELLASRRQINQLLNWhwklkPQNNLPELISGWRGELMAEALHNLLQEY 373
Cdd:COG0349 321 APELLASRKDLEALARW-----GELADPPLLSGWRRELFGEELLALLEGE 365
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 11-187 2.65e-80

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: 243.59  E-value: 2.65e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       11 ALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSEDLEVFL 90
Cdd:cd06142   1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       91 NVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVET 170
Cdd:cd06142  81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160

                       170
                ....*....|....*..
1YT3_A      171 EASGWLPAALDECRLMQ 187
Cdd:cd06142 161 EEEGRLEWAEEECELLL 177
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 3-171 2.42e-62

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: 197.52  E-value: 2.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          3 YQMITTDDALASLCEAVRAFPAIALDTEF--VRTRTYYPQLGLIQLFDGEHLALIDPLGITDW--SPLKAILRDPSITKF 78
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         79 LHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWY 158
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
1YT3_A        159 LLPITAKLMVETE 171
Cdd:pfam01612 161 LLRLYDKLRKELE 173
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 3-171 2.24e-41

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: 143.27  E-value: 2.24e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A           3 YQMITTDDALASLCEAVR-AFPAIALDTEFVRTRTYYPQLGLIQL-FDGEHLALIDPL-GITDWSPLKAILRDPSITKFL 79
Cdd:smart00474   1 VIVVTDSETLEELLEKLRaAGGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLaLGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          80 HAGSEDLEVFLNvFGELPQPLIDTQILAA-FCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWY 158
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYlLLGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|...
1YT3_A         159 LLPITAKLMVETE 171
Cdd:smart00474 160 LLRLYEKLEKELE 172
 
Name Accession Description Interval E-value
PRK10829 PRK10829
ribonuclease D; Provisional
 1-373 0e+00

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 805.38  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         1 MNYQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLH 80
Cdd:PRK10829   1 MNYQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        81 AGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLL 160
Cdd:PRK10829  81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       161 PITAKLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
Cdd:PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       241 EEHLWSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSET 320
Cdd:PRK10829 241 EEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAFKAIKALIQEVSET 320

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
1YT3_A       321 HKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALHNLLQEY 373
Cdd:PRK10829 321 HGLSAELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLAEALTEILQEY 373
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 5-372 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: 585.20  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          5 MITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSE 84
Cdd:TIGR01388   1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         85 DLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITA 164
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        165 KLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        245 WSVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKIS 324
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
1YT3_A        325 AELLASRRQINQLLNWHWKLKPqNNLPELISGWRGELMAEALHNLLQE 372
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKP-NALPPLLQGWRRELGEEALKNLLSE 367
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
5-373 2.94e-171

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 481.68  E-value: 2.94e-171
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        5 MITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSE 84
Cdd:COG0349   1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       85 DLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITA 164
Cdd:COG0349  81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A      165 KLMVETEASGWLPAALDECRLMQMRRQEVVAPEDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A      245 WSVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVEKAQTLPEDALPQPMLNLMDMPGYRKAFKAIKSLITDVSETHKI 323
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|
1YT3_A      324 SAELLASRRQINQLLNWhwklkPQNNLPELISGWRGELMAEALHNLLQEY 373
Cdd:COG0349 321 APELLASRKDLEALARW-----GELADPPLLSGWRRELFGEELLALLEGE 365
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 11-187 2.65e-80

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: 243.59  E-value: 2.65e-80
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       11 ALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSPLKAILRDPSITKFLHAGSEDLEVFL 90
Cdd:cd06142   1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       91 NVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVET 170
Cdd:cd06142  81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160

                       170
                ....*....|....*..
1YT3_A      171 EASGWLPAALDECRLMQ 187
Cdd:cd06142 161 EEEGRLEWAEEECELLL 177
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 11-168 1.81e-76

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: 233.17  E-value: 1.81e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       11 ALASLCEAVR-AFPAIALDTEFVRTRTYYPQLGLIQLF-DGEHLALIDPLGIT-DWSPLKAILRDPSITKFLHAGSEDLE 87
Cdd:cd06129   1 ALSSLCEDLSmDGDVIAFDMEWPPGRRYYGEVALIQLCvSEEKCYLFDPLSLSvDWQGLKMLLENPSIVKALHGIEGDLW 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       88 VFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLM 167
Cdd:cd06129  81 KLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160


                .
1YT3_A      168 V 168
Cdd:cd06129 161 N 161
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 24-168 1.56e-66

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: 207.48  E-value: 1.56e-66
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       24 AIALDTEFVRTRTYYPQLGLIQLFDGE-HLALIDPLGIT-DWSPLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLI 101
Cdd:cd09018   1 VFAFDTETDSLDNISANLVLIQLAIEPgVAALIPVAHDYlALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A      102 DTQILAAFCGRP-MSWGFASMVEEYSGVTLDKSESRTD--WLARPLTERQCEYAAADVWYLLPITAKLMV 168
Cdd:cd09018  81 DTMLEAYILNSVaGRWDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 3-171 2.42e-62

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: 197.52  E-value: 2.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          3 YQMITTDDALASLCEAVRAFPAIALDTEF--VRTRTYYPQLGLIQLFDGEHLALIDPLGITDW--SPLKAILRDPSITKF 78
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         79 LHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWY 158
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160

                         170
                  ....*....|...
1YT3_A        159 LLPITAKLMVETE 171
Cdd:pfam01612 161 LLRLYDKLRKELE 173
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 3-171 2.24e-41

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: 143.27  E-value: 2.24e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A           3 YQMITTDDALASLCEAVR-AFPAIALDTEFVRTRTYYPQLGLIQL-FDGEHLALIDPL-GITDWSPLKAILRDPSITKFL 79
Cdd:smart00474   1 VIVVTDSETLEELLEKLRaAGGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLaLGDDLEILKDLLEDETITKVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A          80 HAGSEDLEVFLNvFGELPQPLIDTQILAA-FCGRPMSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWY 158
Cdd:smart00474  81 HNAKFDLHVLAR-FGIELENIFDTMLAAYlLLGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159

                          170
                   ....*....|...
1YT3_A         159 LLPITAKLMVETE 171
Cdd:smart00474 160 LLRLYEKLEKELE 172
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 7-157 1.20e-19

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: 84.94  E-value: 1.20e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        7 TTDDALASLCEAvraFPAIALDTEFV--RTRTYYPQLGLIQLFDGEHLALIDPLGITDWSP-LKAILRDPSITKFLHAGS 83
Cdd:cd06141   6 DAEEAVKELLGK---EKVVGFDTEWRpsFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPsLKQLLEDPSILKVGVGIK 82

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1YT3_A       84 EDLEVFLNVFGELPQPLIDTQILAA-FCGRPMSWGFASMVEEYSGVTLDKSES--RTDWLARPLTERQCEYAAADVW 157
Cdd:cd06141  83 GDARKLARDFGIEVRGVVDLSHLAKrVGPRRKLVSLARLVEEVLGLPLSKPKKvrCSNWEARPLSKEQILYAATDAY 159
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 5-166 5.31e-19

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: 83.88  E-value: 5.31e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        5 MITTDDALASLCEAV--RAFPAIALDTEF--VRTRTYYPQLGLIQLFDGEHLALID-----PLGITDWS-PLKAILRDPS 74
Cdd:cd06146   3 IVDSEEELEALLLALslEAGRVVGIDSEWkpSFLGDSDPRVAILQLATEDEVFLLDllaleNLESEDWDrLLKRLFEDPD 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       75 ITKFLHAGSEDLEVF------LNVFGELPQPLIDTQILA-AFCGRPMSW----------GFASMVEEYSGVTLDKSESRT 137
Cdd:cd06146  83 VLKLGFGFKQDLKALsasypaLKCMFERVQNVLDLQNLAkELQKSDMGRlkgnlpsktkGLADLVQEVLGKPLDKSEQCS 162

                       170       180
                ....*....|....*....|....*....
1YT3_A      138 DWLARPLTERQCEYAAADVWYLLPITAKL 166
Cdd:cd06146 163 NWERRPLREEQILYAALDAYCLLEVFDKL 191
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
 210-289 1.11e-18

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: 79.65  E-value: 1.11e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         210 RTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARYMPGSLGELDSLGLSGSEIRFH-GKTLLALVEKAQTLPED 288
Cdd:smart00341   1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRyGKDLLAVIQEASDSPSE 80


                   .
1YT3_A         289 A 289
Cdd:smart00341  81 A 81
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 25-108 6.43e-15

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: 69.78  E-value: 6.43e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       25 IALDTEFVRTRTYYPQLGLIQLFDG--EHLALIDplgitdwspLKAILRDPS-ITKFLHAGSEDLEVFLNVFGE------ 95
Cdd:cd06125   1 IAIDTEATGLDGAVHEIIEIALADVnpEDTAVID---------LKDILRDKPlAILVGHNGSFDLPFLNNRCAElglkyp 71

                        90
                ....*....|....
1YT3_A       96 -LPQPLIDTQILAA 108
Cdd:cd06125  72 lLAGSWIDTIKLAA 85
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 3-189 8.73e-15

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: 72.25  E-value: 8.73e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        3 YQMITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWSP-LKAILRDPSITKFLHA 81
Cdd:cd06147   5 LTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHiLNEVFTDPNILKVFHG 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       82 GSEDLEVFLNVFGELPQPLIDTQILAAFCGRPmSWGFASMVEEYSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLP 161
Cdd:cd06147  85 ADSDIIWLQRDFGLYVVNLFDTGQAARVLNLP-RHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLY 163

                       170       180
                ....*....|....*....|....*....
1YT3_A      162 ITAKLMVE-TEASGWLPAALDECRLMQMR 189
Cdd:cd06147 164 IYDRLRNElLERANALAPNLLESVLNCSR 192
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
 213-279 2.33e-14

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: 67.18  E-value: 2.33e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
1YT3_A        213 QLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALV 279
Cdd:pfam00570   1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIpGVGPRKVERYGEEILAAI 68
PRK05755 PRK05755
DNA polymerase I; Provisional
 2-172 1.87e-08

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 56.25  E-value: 1.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A         2 NYQMITTDDALASLCEAVRAFPAIALDTEfvrTRTYYPQ----LGLIQLFDGEHLALIDPLGITDW--SPLKAILRDPSI 75
Cdd:PRK05755 295 DYETILDEEELEAWLAKLKAAGLFAFDTE---TTSLDPMqaelVGLSFAVEPGEAAYIPLDQLDREvlAALKPLLEDPAI 371

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        76 TKFLHAGSEDLEVFLNVFGELPQPLIDTQiLAAFCGRP-MSWGFASMVEEYSGVTLDKSESRT---DWLARPLTERQCEY 151
Cdd:PRK05755 372 KKVGQNLKYDLHVLARYGIELRGIAFDTM-LASYLLDPgRRHGLDSLAERYLGHKTISFEEVAgkqLTFAQVDLEEAAEY 450

                        170       180
                 ....*....|....*....|.
1YT3_A       152 AAADVWYLLPITAKLMVETEA 172
Cdd:PRK05755 451 AAEDADVTLRLHEVLKPKLLE 471
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 66-167 4.13e-05

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: 44.20  E-value: 4.13e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A       66 LKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGR-------PMSW-GFASMVEEYSGVTLDKSESRT 137
Cdd:cd06148  57 LKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALLQEqetggfnPDRViSLVQLLDKYLYISISLKEDVK 136

                        90       100       110
                ....*....|....*....|....*....|....*...
1YT3_A      138 D--------WLARPLTERQCEYAAADVWYLLPITAKLM 167
Cdd:cd06148 137 KlmredpkfWALRPLTEDMIRYAALDVLCLLPLYYAML 174
PRK14975 PRK14975
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
 67-166 2.27e-03

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


Pssm-ID: 237876 [Multi-domain]  Cd Length: 553  Bit Score: 39.97  E-value: 2.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1YT3_A        67 KAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDT----QILAAFCGRPMSwGFASMVEEYSGVTLDKSESRTDWLAr 142
Cdd:PRK14975  39 AAAQEGEEEPRWVWASTAALYPRLLAAGVRVERCHDLmlasQLLLGSEGRAGS-SLSAAAARALGEGLDKPPQTSALSD- 116

                         90       100
                 ....*....|....*....|....
1YT3_A       143 PLTERQCEYAAADVWYLLPITAKL 166
Cdd:PRK14975 117 PPDEEQLLYAAADADVLLELYAVL 140
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 66-107 5.62e-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: 37.50  E-value: 5.62e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
1YT3_A       66 LKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILA 107
Cdd:cd06139  59 LKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTMLAS 100
 
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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