|
Name |
Accession |
Description |
Interval |
E-value |
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
5-364 |
3.13e-154 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 438.15 E-value: 3.13e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 5 IITDNQTLADFCQ--TNASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGE 82
Cdd:COG0349 1 LITTDEELAALCArlAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 83 DLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQ 162
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 163 KLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVREAHL 242
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 243 LRVAERAPQSLTDLNRL-GLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEASGV 320
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEeLPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1381975559 321 PAELIASKRLIHQYLSWKwrleesEDALPALLQGWRGELLQSRL 364
Cdd:COG0349 321 APELLASRKDLEALARWG------ELADPPLLSGWRRELFGEEL 358
|
|
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
1-364 |
2.86e-139 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 400.53 E-value: 2.86e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 1 MTYTIITDNQTLADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLH 78
Cdd:PRK10829 1 MNYQMITTDDALASVCEAarAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 79 AGGEDLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLY 158
Cdd:PRK10829 81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 159 PLYQKLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVR 238
Cdd:PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 239 EAHLLRVAERAPQSLTDLNRLGLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEA 317
Cdd:PRK10829 241 EEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEaLPPPVLNLIDMPGYRKAFKAIKALIQEVSET 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*..
gi 1381975559 318 SGVPAELIASKRLIHQYLSWKWRLeESEDALPALLQGWRGELLQSRL 364
Cdd:PRK10829 321 HGLSAELLASRRQINQLLNWHWKL-KPQNGLPELISGWRGELLAEAL 366
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
5-364 |
5.32e-129 |
|
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: 374.11 E-value: 5.32e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 5 IITDNQTLADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGE 82
Cdd:TIGR01388 1 WITTDDELATVCEAvrTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 83 DLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQ 162
Cdd:TIGR01388 81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 163 KLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVREAHL 242
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 243 LRVAERAPQSLTDLNRLGLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEASGVP 321
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDaLPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320
|
330 340 350 360
....*....|....*....|....*....|....*....|...
gi 1381975559 322 AELIASKRLIHQYLSWKWRLEESedALPALLQGWRGELLQSRL 364
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKPN--ALPPLLQGWRRELGEEAL 361
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
12-182 |
1.71e-74 |
|
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: 228.19 E-value: 1.71e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 12 LADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGEDLELFQH 89
Cdd:cd06142 2 LEDLCERlaSAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 90 QSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQKLHEQLA 169
Cdd:cd06142 82 DFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161
|
170
....*....|...
gi 1381975559 170 QKGLLDWFEQECE 182
Cdd:cd06142 162 EEGRLEWAEEECE 174
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
3-168 |
4.95e-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: 142.06 E-value: 4.95e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 3 YTIITDNQTLADFCQ--TNASVLAIDTEF--VRTRTYYARPGLYQINDGERTALVDPLAVTD--MSPLWRLLHDSGRLCL 76
Cdd:pfam01612 1 YRIVTTEDELEDLIEelLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDdvLSALKRLLEDPNITKV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 77 LHAGGEDLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIY 156
Cdd:pfam01612 81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160
|
170
....*....|..
gi 1381975559 157 LYPLYQKLHEQL 168
Cdd:pfam01612 161 LLRLYDKLRKEL 172
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
3-169 |
4.05e-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: 4.05e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 3 YTIITDNQTLADFC---QTNASVLAIDTEFVRTRTYYARPGLYQI-NDGERTALVDPLAV-TDMSPLWRLLHDSGRLCLL 77
Cdd:smart00474 1 VIVVTDSETLEELLeklRAAGGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLALgDDLEILKDLLEDETITKVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 78 HAGGEDLELFQHQsGALPARVHDTQLAAA-FLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIY 156
Cdd:smart00474 81 HNAKFDLHVLARF-GIELENIFDTMLAAYlLLGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
170
....*....|...
gi 1381975559 157 LYPLYQKLHEQLA 169
Cdd:smart00474 160 LLRLYEKLEKELE 172
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
5-364 |
3.13e-154 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 438.15 E-value: 3.13e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 5 IITDNQTLADFCQ--TNASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGE 82
Cdd:COG0349 1 LITTDEELAALCArlAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 83 DLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQ 162
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 163 KLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVREAHL 242
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 243 LRVAERAPQSLTDLNRL-GLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEASGV 320
Cdd:COG0349 241 LELARRQPKSLEELARLrGLSPGEIRRHGEELLAAVAEALALPEEeLPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1381975559 321 PAELIASKRLIHQYLSWKwrleesEDALPALLQGWRGELLQSRL 364
Cdd:COG0349 321 APELLASRKDLEALARWG------ELADPPLLSGWRRELFGEEL 358
|
|
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
1-364 |
2.86e-139 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 400.53 E-value: 2.86e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 1 MTYTIITDNQTLADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLH 78
Cdd:PRK10829 1 MNYQMITTDDALASVCEAarAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 79 AGGEDLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLY 158
Cdd:PRK10829 81 AGSEDLEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 159 PLYQKLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVR 238
Cdd:PRK10829 161 PIAAKLMAETEAAGWLPAALDECRLLCQRRQEVLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 239 EAHLLRVAERAPQSLTDLNRLGLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEA 317
Cdd:PRK10829 241 EEHLWQVARYMPGSLGELDSLGLSGSEIRFHGKTLLALVAKAQALPEEaLPPPVLNLIDMPGYRKAFKAIKALIQEVSET 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*..
gi 1381975559 318 SGVPAELIASKRLIHQYLSWKWRLeESEDALPALLQGWRGELLQSRL 364
Cdd:PRK10829 321 HGLSAELLASRRQINQLLNWHWKL-KPQNGLPELISGWRGELLAEAL 366
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
5-364 |
5.32e-129 |
|
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: 374.11 E-value: 5.32e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 5 IITDNQTLADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGE 82
Cdd:TIGR01388 1 WITTDDELATVCEAvrTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 83 DLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQ 162
Cdd:TIGR01388 81 DLEVFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 163 KLHEQLAQKGLLDWFEQECEWAVKRRSVSVKPELAYLEAKNAWTLDRQALGILQRLCEWRLNEARRRDLAVNFVVREAHL 242
Cdd:TIGR01388 161 KLMERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 243 LRVAERAPQSLTDLNRLGLEPMEIKRHGQTLLALVQQALAAPES-WPEPVQRLVDFPGYKAELKRIRGLVEQAGEASGVP 321
Cdd:TIGR01388 241 WELARQAPGNLTELASLGPKGSEIRKHGDTLLALVKTALALPEDaLPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLA 320
|
330 340 350 360
....*....|....*....|....*....|....*....|...
gi 1381975559 322 AELIASKRLIHQYLSWKWRLEESedALPALLQGWRGELLQSRL 364
Cdd:TIGR01388 321 SELLASRRQLEQLLAWGWKLKPN--ALPPLLQGWRRELGEEAL 361
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
12-182 |
1.71e-74 |
|
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: 228.19 E-value: 1.71e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 12 LADFCQT--NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAVTDMSPLWRLLHDSGRLCLLHAGGEDLELFQH 89
Cdd:cd06142 2 LEDLCERlaSAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 90 QSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQKLHEQLA 169
Cdd:cd06142 82 DFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161
|
170
....*....|...
gi 1381975559 170 QKGLLDWFEQECE 182
Cdd:cd06142 162 EEGRLEWAEEECE 174
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
3-168 |
4.95e-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: 142.06 E-value: 4.95e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 3 YTIITDNQTLADFCQ--TNASVLAIDTEF--VRTRTYYARPGLYQINDGERTALVDPLAVTD--MSPLWRLLHDSGRLCL 76
Cdd:pfam01612 1 YRIVTTEDELEDLIEelLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDdvLSALKRLLEDPNITKV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 77 LHAGGEDLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIY 156
Cdd:pfam01612 81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160
|
170
....*....|..
gi 1381975559 157 LYPLYQKLHEQL 168
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 ... |
12-164 |
2.63e-35 |
|
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: 126.86 E-value: 2.63e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 12 LADFCQ---TNASVLAIDTEFVRTRTYYARPGLYQI-NDGERTALVDPLAVT-DMSPLWRLLHDSGRLCLLHAGGEDLEL 86
Cdd:cd06129 2 LSSLCEdlsMDGDVIAFDMEWPPGRRYYGEVALIQLcVSEEKCYLFDPLSLSvDWQGLKMLLENPSIVKALHGIEGDLWK 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1381975559 87 FQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQKL 164
Cdd:cd06129 82 LLRDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
3-169 |
4.05e-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: 4.05e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 3 YTIITDNQTLADFC---QTNASVLAIDTEFVRTRTYYARPGLYQI-NDGERTALVDPLAV-TDMSPLWRLLHDSGRLCLL 77
Cdd:smart00474 1 VIVVTDSETLEELLeklRAAGGEVALDTETTGLDSYSGKLVLIQIsVTGEGAFIIDPLALgDDLEILKDLLEDETITKVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 78 HAGGEDLELFQHQsGALPARVHDTQLAAA-FLGLGTQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIY 156
Cdd:smart00474 81 HNAKFDLHVLARF-GIELENIFDTMLAAYlLLGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
170
....*....|...
gi 1381975559 157 LYPLYQKLHEQLA 169
Cdd:smart00474 160 LLRLYEKLEKELE 172
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
22-164 |
5.19e-24 |
|
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: 96.15 E-value: 5.19e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 22 VLAIDTEFVRTRTYYARPGLYQINDGE-RTALVDPLAVT-DMSPLWRLLHDSGRLCLLHAGGEDLELFQHQSGALPARVH 99
Cdd:cd09018 1 VFAFDTETDSLDNISANLVLIQLAIEPgVAALIPVAHDYlALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAF 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1381975559 100 DTQLAAAFLGLGTQL-GFAPLVEQLLGVSLDKAHARTD--WLARPLSAAQLSYAADDVIYLYPLYQKL 164
Cdd:cd09018 81 DTMLEAYILNSVAGRwDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
212-277 |
5.44e-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: 66.02 E-value: 5.44e-14
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1381975559 212 LGILQRLCEWRLNEARRRDLAVNFVVREAHLLRVAERAPQSLTDLNRL-GLEPMEIKRHGQTLLALV 277
Cdd:pfam00570 2 LALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIpGVGPRKVERYGEEILAAI 68
|
|
| Rrp6p_like_exo |
cd06147 |
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ... |
19-172 |
9.36e-14 |
|
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: 69.16 E-value: 9.36e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 19 NASVLAIDTEFVRTRTYYARPGLYQINDGERTALVDPLAV-TDMSPLWRLLHDSGRLCLLHAGGEDLELFQHQSGALPAR 97
Cdd:cd06147 23 NCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLrDDMHILNEVFTDPNILKVFHGADSDIIWLQRDFGLYVVN 102
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1381975559 98 VHDTQLAAAFLGLGtQLGFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQKLHEQLAQKG 172
Cdd:cd06147 103 LFDTGQAARVLNLP-RHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHYLLYIYDRLRNELLERA 176
|
|
| WRN_exo |
cd06141 |
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ... |
6-164 |
2.89e-10 |
|
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: 58.36 E-value: 2.89e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 6 ITDNQTLADFCQ---TNASVLAIDTEFVRTRTYYARPG--LYQINDGERTALVDPLAVTDMSP-LWRLLHDSGRLCLLHA 79
Cdd:cd06141 1 TDSAQDAEEAVKellGKEKVVGFDTEWRPSFRKGKRNKvaLLQLATESRCLLFQLAHMDKLPPsLKQLLEDPSILKVGVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 80 GGEDLELFQHQSGALPARVHDTQ-LAAAFLGLGTQLGFAPLVEQLLGVSLDK--AHARTDWLARPLSAAQLSYAADDVIY 156
Cdd:cd06141 81 IKGDARKLARDFGIEVRGVVDLShLAKRVGPRRKLVSLARLVEEVLGLPLSKpkKVRCSNWEARPLSKEQILYAATDAYA 160
|
....*...
gi 1381975559 157 LYPLYQKL 164
Cdd:cd06141 161 SLELYRKL 168
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
208-285 |
3.17e-09 |
|
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: 53.07 E-value: 3.17e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1381975559 208 DRQALGILQRLCEWRLNEARRRDLAVNFVVREAHLLRVAERAPQSLTDLNRL-GLEPMEIKRHGQTLLALVQQALAAPE 285
Cdd:smart00341 1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIdGVGEEKARRYGKDLLAVIQEASDSPS 79
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
92-170 |
2.32e-07 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 52.30 E-value: 2.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 92 GALPARVHDTQLAAAFLGLGTQLGFAPL---VEQLLGVSLDKAHARTDWLArPLSAAQLSYAADDVIYLYPLYQKLHEQL 168
Cdd:PRK14975 66 GVRVERCHDLMLASQLLLGSEGRAGSSLsaaAARALGEGLDKPPQTSALSD-PPDEEQLLYAAADADVLLELYAVLADQL 144
|
..
gi 1381975559 169 AQ 170
Cdd:PRK14975 145 NR 146
|
|
| mut-7_like_exo |
cd06146 |
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ... |
115-166 |
2.79e-07 |
|
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: 50.37 E-value: 2.79e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 1381975559 115 GFAPLVEQLLGVSLDKAHARTDWLARPLSAAQLSYAADDVIYLYPLYQKLHE 166
Cdd:cd06146 142 GLADLVQEVLGKPLDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKLLE 193
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
76-184 |
6.33e-07 |
|
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: 49.21 E-value: 6.33e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 76 LLHAGGEDLELFQHQSGALPARVHDTQLAAAFL----GLG----TQLGFAPLVEQLLGVS---LDKAH--ARTD---WLA 139
Cdd:cd06148 69 VIHDCRRDSDALYHQYGIKLNNVFDTQVADALLqeqeTGGfnpdRVISLVQLLDKYLYISislKEDVKklMREDpkfWAL 148
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1381975559 140 RPLSAAQLSYAADDVIYLYPLYQKLHEQLAQKGLLDWFEQECEWA 184
Cdd:cd06148 149 RPLTEDMIRYAALDVLCLLPLYYAMLDALISKFLKAVFKYLNTER 193
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
3-179 |
1.21e-04 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 43.93 E-value: 1.21e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 3 YTIITDNQTLADFCQ--TNASVLAIDTEfvrTRTYYARP----GLYQINDGERTALVDP--LAVTDMSPLWRLLHDSGRL 74
Cdd:PRK05755 296 YETILDEEELEAWLAklKAAGLFAFDTE---TTSLDPMQaelvGLSFAVEPGEAAYIPLdqLDREVLAALKPLLEDPAIK 372
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1381975559 75 CLLHAGGEDLELFQHQSGALPARVHDTQLAAAFLGLGTQLGFAPLVEQLLG---VSLDKAHARTDWLARPLSAAQLSYAA 151
Cdd:PRK05755 373 KVGQNLKYDLHVLARYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGhktISFEEVAGKQLTFAQVDLEEAAEYAA 452
|
170 180
....*....|....*....|....*....
gi 1381975559 152 DDVIYLYPLYQKLHEQLAQK-GLLDWFEQ 179
Cdd:PRK05755 453 EDADVTLRLHEVLKPKLLEEpGLLELYEE 481
|
|
| |
