|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
1-369 |
0e+00 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 772.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:PRK10829 5 MITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGSE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:PRK10829 85 DLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAA 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:PRK10829 165 KLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGMGLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKIS 320
Cdd:PRK10829 245 WQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAFKAIKALIQEVSETHGLS 324
|
330 340 350 360
....*....|....*....|....*....|....*....|....*....
gi 501073564 321 AELMASRRQINQLLNWHWKLKPQNQLPELISGWRGELLNESLKTLLENY 369
Cdd:PRK10829 325 AELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLAEALTEILQEY 373
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
1-366 |
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: 508.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:TIGR01388 81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGMGLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKIS 320
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 501073564 321 AELMASRRQINQLLNWHWKLKPqNQLPELISGWRGELLNESLKTLL 366
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKP-NALPPLLQGWRRELGEEALKNLL 365
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
1-369 |
7.57e-176 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 493.24 E-value: 7.57e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:COG0349 1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGM-GLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKI 319
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|
gi 501073564 320 SAELMASRRQINQLLNWhwklkPQNQLPELISGWRGELLNESLKTLLENY 369
Cdd:COG0349 321 APELLASRKDLEALARW-----GELADPPLLSGWRRELFGEELLALLEGE 365
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
7-183 |
2.52e-76 |
|
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: 233.19 E-value: 2.52e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 7 ALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSEDLEVFQ 86
Cdd:cd06142 1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 87 NAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAHKLMEQV 166
Cdd:cd06142 81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160
|
170
....*....|....*..
gi 501073564 167 REAGWLTAAINECRLMT 183
Cdd:cd06142 161 EEEGRLEWAEEECELLL 177
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
1-167 |
4.13e-47 |
|
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: 157.85 E-value: 4.13e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEF--VRTRTYYPQLGLIQLYDGENVALIDPLTITDW--APFQALLQDQNVTKFLH 76
Cdd:pfam01612 3 IVTTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKVGH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 77 AGSEDLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLL 156
Cdd:pfam01612 83 NAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADYLL 162
|
170
....*....|.
gi 501073564 157 PIAHKLMEQVR 167
Cdd:pfam01612 163 RLYDKLRKELE 173
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
1-167 |
3.50e-33 |
|
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: 121.69 E-value: 3.50e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQ-RALALDTEFVRTRTYYPQLGLIQL-YDGENVALIDPLTI-TDWAPFQALLQDQNVTKFLHA 77
Cdd:smart00474 3 VVTDSETLEELLEKLRAAgGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLALgDDLEILKDLLEDETITKVGHN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 78 GSEDLEVFQNaFSMMPDPFIDTQVLASFVGHPLSC-GFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLL 156
Cdd:smart00474 83 AKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSKhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADALL 161
|
170
....*....|.
gi 501073564 157 PIAHKLMEQVR 167
Cdd:smart00474 162 RLYEKLEKELE 172
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
1-369 |
0e+00 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 772.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:PRK10829 5 MITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGSE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:PRK10829 85 DLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAA 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:PRK10829 165 KLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHL 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGMGLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKIS 320
Cdd:PRK10829 245 WQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEALPPPVLNLIDMPGYRKAFKAIKALIQEVSETHGLS 324
|
330 340 350 360
....*....|....*....|....*....|....*....|....*....
gi 501073564 321 AELMASRRQINQLLNWHWKLKPQNQLPELISGWRGELLNESLKTLLENY 369
Cdd:PRK10829 325 AELLASRRQINQLLNWHWKLKPQNGLPELISGWRGELLAEALTEILQEY 373
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
1-366 |
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: 508.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:TIGR01388 81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGMGLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKIS 320
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 501073564 321 AELMASRRQINQLLNWHWKLKPqNQLPELISGWRGELLNESLKTLL 366
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKP-NALPPLLQGWRRELGEEALKNLL 365
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
1-369 |
7.57e-176 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 493.24 E-value: 7.57e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSE 80
Cdd:COG0349 1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 81 DLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAH 160
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 161 KLMEQVREAGWLTAAINECRLMTQRRGEVLDPDEAWREITNAWQLRPRQLACLKLLAGWRLRKARERDMAVNFVVREENL 240
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 241 WKVARHMPGSLGELDGM-GLSGSEIRFHGKTLLALVAQAQALPEEALPEPLANLVDMPGYRKVFKEIKALVQATSEAHKI 319
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|
gi 501073564 320 SAELMASRRQINQLLNWhwklkPQNQLPELISGWRGELLNESLKTLLENY 369
Cdd:COG0349 321 APELLASRKDLEALARW-----GELADPPLLSGWRRELFGEELLALLEGE 365
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
7-183 |
2.52e-76 |
|
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: 233.19 E-value: 2.52e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 7 ALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTITDWAPFQALLQDQNVTKFLHAGSEDLEVFQ 86
Cdd:cd06142 1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 87 NAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAHKLMEQV 166
Cdd:cd06142 81 RDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEEL 160
|
170
....*....|....*..
gi 501073564 167 REAGWLTAAINECRLMT 183
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 ... |
7-163 |
8.24e-55 |
|
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: 177.32 E-value: 8.24e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 7 ALATLCETARTQ-RALALDTEFVRTRTYYPQLGLIQLY-DGENVALIDPLTIT-DWAPFQALLQDQNVTKFLHAGSEDLE 83
Cdd:cd06129 1 ALSSLCEDLSMDgDVIAFDMEWPPGRRYYGEVALIQLCvSEEKCYLFDPLSLSvDWQGLKMLLENPSIVKALHGIEGDLW 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 84 VFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLLPIAHKLM 163
Cdd:cd06129 81 KLLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
20-163 |
1.17e-47 |
|
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: 158.56 E-value: 1.17e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 20 ALALDTEFVRTRTYYPQLGLIQLYDGENV-ALIDPLTIT-DWAPFQALLQDQNVTKFLHAGSEDLEVFQNAFSMMPDPFI 97
Cdd:cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPGVaALIPVAHDYlALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501073564 98 DTQVLASFVGHP-LSCGFATLVEHHTGVVLDKSESRTD--WLARPLTERQCDYAAADVWYLLPIAHKLM 163
Cdd:cd09018 81 DTMLEAYILNSVaGRWDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKLW 149
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
1-167 |
4.13e-47 |
|
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: 157.85 E-value: 4.13e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEF--VRTRTYYPQLGLIQLYDGENVALIDPLTITDW--APFQALLQDQNVTKFLH 76
Cdd:pfam01612 3 IVTTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDDvlSALKRLLEDPNITKVGH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 77 AGSEDLEVFQNAFSMMPDPFIDTQVLASFVGHPLSCGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLL 156
Cdd:pfam01612 83 NAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADYLL 162
|
170
....*....|.
gi 501073564 157 PIAHKLMEQVR 167
Cdd:pfam01612 163 RLYDKLRKELE 173
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
1-167 |
3.50e-33 |
|
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: 121.69 E-value: 3.50e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQ-RALALDTEFVRTRTYYPQLGLIQL-YDGENVALIDPLTI-TDWAPFQALLQDQNVTKFLHA 77
Cdd:smart00474 3 VVTDSETLEELLEKLRAAgGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLALgDDLEILKDLLEDETITKVGHN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 78 GSEDLEVFQNaFSMMPDPFIDTQVLASFVGHPLSC-GFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVWYLL 156
Cdd:smart00474 83 AKFDLHVLAR-FGIELENIFDTMLAAYLLLGGPSKhGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADALL 161
|
170
....*....|.
gi 501073564 157 PIAHKLMEQVR 167
Cdd:smart00474 162 RLYEKLEKELE 172
|
|
| mut-7_like_exo |
cd06146 |
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ... |
14-164 |
2.73e-18 |
|
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: 81.96 E-value: 2.73e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 14 TARTQRALALDTEF--VRTRTYYPQLGLIQLYDGENVALIDPLTIT-----DWAPF-QALLQDQNVTKFLHAGSEDLEVF 85
Cdd:cd06146 18 SLEAGRVVGIDSEWkpSFLGDSDPRVAILQLATEDEVFLLDLLALEnleseDWDRLlKRLFEDPDVLKLGFGFKQDLKAL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 86 QNAFSM------MPDPFIDTQVLA---------SFVGHPLS--CGFATLVEHHTGVVLDKSESRTDWLARPLTERQCDYA 148
Cdd:cd06146 98 SASYPAlkcmfeRVQNVLDLQNLAkelqksdmgRLKGNLPSktKGLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYA 177
|
170
....*....|....*.
gi 501073564 149 AADVWYLLPIAHKLME 164
Cdd:cd06146 178 ALDAYCLLEVFDKLLE 193
|
|
| WRN_exo |
cd06141 |
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ... |
18-164 |
2.02e-14 |
|
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: 70.30 E-value: 2.02e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 18 QRALALDTEFV--RTRTYYPQLGLIQLYDGENVALIDPLTITDWAP-FQALLQDQNVTKFLHAGSEDLEVFQNAFSMMPD 94
Cdd:cd06141 18 EKVVGFDTEWRpsFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPsLKQLLEDPSILKVGVGIKGDARKLARDFGIEVR 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501073564 95 PFIDTQVLASFVGHPLS-CGFATLVEHHTGVVLDKSES--RTDWLARPLTERQCDYAAADVWYLLPIAHKLME 164
Cdd:cd06141 98 GVVDLSHLAKRVGPRRKlVSLARLVEEVLGLPLSKPKKvrCSNWEARPLSKEQILYAATDAYASLELYRKLLA 170
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
206-285 |
2.50e-13 |
|
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: 64.63 E-value: 2.50e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 206 RPRQLACLKLLAGWRLRKARERDMAVNFVVREENLWKVARHMPGSLGELDGMGLSGSEIRFH-GKTLLALVAQAQALPEE 284
Cdd:smart00341 1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRyGKDLLAVIQEASDSPSE 80
|
.
gi 501073564 285 A 285
Cdd:smart00341 81 A 81
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
209-275 |
3.48e-13 |
|
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: 64.09 E-value: 3.48e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501073564 209 QLACLKLLAGWRLRKARERDMAVNFVVREENLWKVARHMPGSLGELDGM-GLSGSEIRFHGKTLLALV 275
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIpGVGPRKVERYGEEILAAI 68
|
|
| Rrp6p_like_exo |
cd06147 |
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ... |
1-162 |
1.34e-12 |
|
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: 65.70 E-value: 1.34e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 1 MITTNDALATLCETARTQRALALDTEFVRTRTYYPQLGLIQLYDGENVALIDPLTItdWAPFQAL---LQDQNVTKFLHA 77
Cdd:cd06147 7 FVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKL--RDDMHILnevFTDPNILKVFHG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 78 GSEDLEVFQNAFSM----MPDPFIDTQVLaSFVGHPLscgfATLVEHHTGVVLDKSESRTDWLARPLTERQCDYAAADVW 153
Cdd:cd06147 85 ADSDIIWLQRDFGLyvvnLFDTGQAARVL-NLPRHSL----AYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTH 159
|
....*....
gi 501073564 154 YLLPIAHKL 162
Cdd:cd06147 160 YLLYIYDRL 168
|
|
| DnaQ_like_exo |
cd06125 |
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ... |
22-103 |
4.71e-09 |
|
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: 53.21 E-value: 4.71e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 22 ALDTEFVRTRTYYPQLGLIQLYDG--ENVALIDpltitdwapFQALLQDQ-NVTKFLHAGSEDLEVFQNAF-------SM 91
Cdd:cd06125 2 AIDTEATGLDGAVHEIIEIALADVnpEDTAVID---------LKDILRDKpLAILVGHNGSFDLPFLNNRCaelglkyPL 72
|
90
....*....|..
gi 501073564 92 MPDPFIDTQVLA 103
Cdd:cd06125 73 LAGSWIDTIKLA 84
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
18-165 |
1.88e-08 |
|
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: 53.83 E-value: 1.88e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 18 QRALALDTEFVRTRTYyPQLGLIQL-YDGENVALIDpLTITDWAPF----QALLQDQNVTKFLHAGSEDLEVFQNAFSMM 92
Cdd:cd06148 10 QKVIGLDCEGVNLGRK-GKLCLVQIaTRTGQIYLFD-ILKLGSIVFinglKDILESKKILKVIHDCRRDSDALYHQYGIK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501073564 93 PDPFIDTQVLASFVGHPLS--------CGFATLVEHHTGV----VLD-KSESRTD---WLARPLTERQCDYAAADVWYLL 156
Cdd:cd06148 88 LNNVFDTQVADALLQEQETggfnpdrvISLVQLLDKYLYIsislKEDvKKLMREDpkfWALRPLTEDMIRYAALDVLCLL 167
|
....*....
gi 501073564 157 PIAHKLMEQ 165
Cdd:cd06148 168 PLYYAMLDA 176
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
107-168 |
3.73e-03 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 39.20 E-value: 3.73e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501073564 107 GHPLScgfaTLVEHHTGVVLDKSESRTDWLArPLTERQCDYAAADVWYLLPIAHKLMEQVRE 168
Cdd:PRK14975 90 GSSLS----AAAARALGEGLDKPPQTSALSD-PPDEEQLLYAAADADVLLELYAVLADQLNR 146
|
|
| |
