|
Name |
Accession |
Description |
Interval |
E-value |
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
5-367 |
2.33e-162 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 459.34 E-value: 2.33e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 5 YLDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQ 84
Cdd:COG0349 1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 85 DLELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYH 164
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 165 QMQQSLTELNRTHWLADDFAALSDPQTYQADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWILKDDVM 244
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 245 LDLARFAPDSLTKLSQIRGLEPRDIDRHGQAILDVLEKASQIPKADWPVMLKPEPLTNQQEALLDALMALLRQFCDEQAI 324
Cdd:COG0349 241 LELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 386271152 325 SPAAVATRKDIEKLVR--GETTIPLLKGWRKQIVGRKLQAFLQGK 367
Cdd:COG0349 321 APELLASRKDLEALARwgELADPPLLSGWRRELFGEELLALLEGE 365
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
8-365 |
1.49e-112 |
|
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: 333.28 E-value: 1.49e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 8 TPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQDLE 87
Cdd:TIGR01388 4 TDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASEDLE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 88 LLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQMQ 167
Cdd:TIGR01388 84 VFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLM 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 168 QSLTELNRTHWLADDFAALSDPQTYQADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWILKDDVMLDL 247
Cdd:TIGR01388 164 ERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWEL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 248 ARFAPDSLTKLSQIrGLEPRDIDRHGQAILDVLEKASQIPKADWPVMLKPEPLTNQQEALLDALMALLRQFCDEQAISPA 327
Cdd:TIGR01388 244 ARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLASE 322
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 386271152 328 AVATRKDIEKLV------RGETTIPLLKGWRKQIVGRKLQAFLQ 365
Cdd:TIGR01388 323 LLASRRQLEQLLawgwklKPNALPPLLQGWRRELGEEALKNLLS 366
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
12-188 |
1.24e-75 |
|
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: 232.04 E-value: 1.24e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 12 LLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQDLELLLM 91
Cdd:cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 92 HRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQMQQSLT 171
Cdd:cd06142 82 DFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161
|
170
....*....|....*..
gi 386271152 172 ELNRTHWLADDFAALSD 188
Cdd:cd06142 162 EEGRLEWAEEECELLLD 178
|
|
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
6-366 |
2.46e-72 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 230.27 E-value: 2.46e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 6 LDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQD 85
Cdd:PRK10829 6 ITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGSED 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 86 LELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQ 165
Cdd:PRK10829 86 LEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 166 MqqsLTELNRTHWLAddfAALSDPQTYQ------ADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWIL 239
Cdd:PRK10829 166 L---MAETEAAGWLP---AALDECRLLCqrrqevLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVV 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 240 KDDVMLDLARFAPDSLTKLSQIrGLEPRDIDRHGQAILDVLEKASQIPKADWpvmlkPEPLTN-----QQEALLDALMAL 314
Cdd:PRK10829 240 REEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEAL-----PPPVLNlidmpGYRKAFKAIKAL 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 386271152 315 LRQFCDEQAISPAAVATRKDIE-------KLVRGETTIPLLKGWRKQIVGRKLQAFLQG 366
Cdd:PRK10829 314 IQEVSETHGLSAELLASRRQINqllnwhwKLKPQNGLPELISGWRGELLAEALTEILQE 372
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
7-167 |
5.28e-38 |
|
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: 134.74 E-value: 5.28e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 7 DTPVGLLDFCQQIQNSSWLAVDTEF--LREKTYYPQLCLIQIANDDVIACIDPLAIDD--LTPLFDVLYQPKMTLVFHAA 82
Cdd:pfam01612 5 TTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDdvLSALKRLLEDPNITKVGHNA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 83 RQDLELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSL 162
Cdd:pfam01612 85 KFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADYLLRL 164
|
....*
gi 386271152 163 YHQMQ 167
Cdd:pfam01612 165 YDKLR 169
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
5-167 |
5.26e-26 |
|
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: 102.82 E-value: 5.26e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 5 YLDTPVGLLDFCQQI-QNSSWLAVDTEFLREKTYYPQLCLIQIA-NDDVIACIDPLAI-DDLTPLFDVLYQPKMTLVFHA 81
Cdd:smart00474 3 VVTDSETLEELLEKLrAAGGEVALDTETTGLDSYSGKLVLIQISvTGEGAFIIDPLALgDDLEILKDLLEDETITKVGHN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 82 ARQDLELLLmHRQQLPDTIFDTQLAASVL-GLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLR 160
Cdd:smart00474 83 AKFDLHVLA-RFGIELENIFDTMLAAYLLlGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADALL 161
|
....*..
gi 386271152 161 SLYHQMQ 167
Cdd:smart00474 162 RLYEKLE 168
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
5-367 |
2.33e-162 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 459.34 E-value: 2.33e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 5 YLDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQ 84
Cdd:COG0349 1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAIGDLSPLWELLADPAIVKVFHAARE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 85 DLELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYH 164
Cdd:COG0349 81 DLEILYHLFGILPKPLFDTQIAAALLGYGDSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLYE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 165 QMQQSLTELNRTHWLADDFAALSDPQTYQADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWILKDDVM 244
Cdd:COG0349 161 KLLEELEREGRLEWAEEECARLLDPATYREDPEEAWLRLKGAWKLNPRQLAVLRELAAWREREARKRDVPRNRVLKDEAL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 245 LDLARFAPDSLTKLSQIRGLEPRDIDRHGQAILDVLEKASQIPKADWPVMLKPEPLTNQQEALLDALMALLRQFCDEQAI 324
Cdd:COG0349 241 LELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALPEEELPEPPRRLPLSPGYKALLKLLKALLKEVAEELGV 320
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 386271152 325 SPAAVATRKDIEKLVR--GETTIPLLKGWRKQIVGRKLQAFLQGK 367
Cdd:COG0349 321 APELLASRKDLEALARwgELADPPLLSGWRRELFGEELLALLEGE 365
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
8-365 |
1.49e-112 |
|
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: 333.28 E-value: 1.49e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 8 TPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQDLE 87
Cdd:TIGR01388 4 TDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVIIDWSPLKELLRDESVVKVLHAASEDLE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 88 LLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQMQ 167
Cdd:TIGR01388 84 VFLNLFGELPQPLFDTQIAAAFCGFGMSMGYAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKLM 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 168 QSLTELNRTHWLADDFAALSDPQTYQADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWILKDDVMLDL 247
Cdd:TIGR01388 164 ERLEESGRLAWLEEECTLLTDRRTYVVNPEDAWRDIKNAWQLRPQQLAVLQALAAWREREARERDLPRNFVLKEEALWEL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 248 ARFAPDSLTKLSQIrGLEPRDIDRHGQAILDVLEKASQIPKADWPVMLKPEPLTNQQEALLDALMALLRQFCDEQAISPA 327
Cdd:TIGR01388 244 ARQAPGNLTELASL-GPKGSEIRKHGDTLLALVKTALALPEDALPQAPLNLMPPPGYKALFKLLKVLVKDVSETLGLASE 322
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 386271152 328 AVATRKDIEKLV------RGETTIPLLKGWRKQIVGRKLQAFLQ 365
Cdd:TIGR01388 323 LLASRRQLEQLLawgwklKPNALPPLLQGWRRELGEEALKNLLS 366
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
12-188 |
1.24e-75 |
|
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: 232.04 E-value: 1.24e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 12 LLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQDLELLLM 91
Cdd:cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAIGDLSPLKELLADPNIVKVFHAAREDLELLKR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 92 HRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQMQQSLT 171
Cdd:cd06142 82 DFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEELE 161
|
170
....*....|....*..
gi 386271152 172 ELNRTHWLADDFAALSD 188
Cdd:cd06142 162 EEGRLEWAEEECELLLD 178
|
|
| PRK10829 |
PRK10829 |
ribonuclease D; Provisional |
6-366 |
2.46e-72 |
|
ribonuclease D; Provisional
Pssm-ID: 236771 [Multi-domain] Cd Length: 373 Bit Score: 230.27 E-value: 2.46e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 6 LDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLAIDDLTPLFDVLYQPKMTLVFHAARQD 85
Cdd:PRK10829 6 ITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDGEQLSLIDPLGITDWSPFKALLRDPQVTKFLHAGSED 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 86 LELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQ 165
Cdd:PRK10829 86 LEVFLNAFGELPQPLIDTQILAAFCGRPLSCGFASMVEEYTGVTLDKSESRTDWLARPLSERQCEYAAADVFYLLPIAAK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 166 MqqsLTELNRTHWLAddfAALSDPQTYQ------ADPETIWRKIRGAGKLKPRQLANLQQLAAWRERNAIQRNRPRRWIL 239
Cdd:PRK10829 166 L---MAETEAAGWLP---AALDECRLLCqrrqevLAPEEAYRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVV 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 240 KDDVMLDLARFAPDSLTKLSQIrGLEPRDIDRHGQAILDVLEKASQIPKADWpvmlkPEPLTN-----QQEALLDALMAL 314
Cdd:PRK10829 240 REEHLWQVARYMPGSLGELDSL-GLSGSEIRFHGKTLLALVAKAQALPEEAL-----PPPVLNlidmpGYRKAFKAIKAL 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 386271152 315 LRQFCDEQAISPAAVATRKDIE-------KLVRGETTIPLLKGWRKQIVGRKLQAFLQG 366
Cdd:PRK10829 314 IQEVSETHGLSAELLASRRQINqllnwhwKLKPQNGLPELISGWRGELLAEALTEILQE 372
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
7-167 |
5.28e-38 |
|
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: 134.74 E-value: 5.28e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 7 DTPVGLLDFCQQIQNSSWLAVDTEF--LREKTYYPQLCLIQIANDDVIACIDPLAIDD--LTPLFDVLYQPKMTLVFHAA 82
Cdd:pfam01612 5 TTEDELEDLIEELLNAPYVAVDTETtsLDTYSYYLRGALIQIGTGEGAYIIDPLALGDdvLSALKRLLEDPNITKVGHNA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 83 RQDLELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSL 162
Cdd:pfam01612 85 KFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRSHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADYLLRL 164
|
....*
gi 386271152 163 YHQMQ 167
Cdd:pfam01612 165 YDKLR 169
|
|
| RNaseD_like |
cd06129 |
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ... |
14-166 |
8.78e-30 |
|
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: 112.61 E-value: 8.78e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 14 DFCQQIQ-NSSWLAVDTEFLREKTYYPQLCLIQIANDDV-IACIDPLAI-DDLTPLFDVLYQPKMTLVFHAARQDLELLL 90
Cdd:cd06129 4 SLCEDLSmDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEkCYLFDPLSLsVDWQGLKMLLENPSIVKALHGIEGDLWKLL 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386271152 91 MHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLRSLYHQM 166
Cdd:cd06129 84 RDFGEKLQRLFDTTIAANLKGLPERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
5-167 |
5.26e-26 |
|
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: 102.82 E-value: 5.26e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 5 YLDTPVGLLDFCQQI-QNSSWLAVDTEFLREKTYYPQLCLIQIA-NDDVIACIDPLAI-DDLTPLFDVLYQPKMTLVFHA 81
Cdd:smart00474 3 VVTDSETLEELLEKLrAAGGEVALDTETTGLDSYSGKLVLIQISvTGEGAFIIDPLALgDDLEILKDLLEDETITKVGHN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 82 ARQDLELLLmHRQQLPDTIFDTQLAASVL-GLGEQVGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADDVRYLR 160
Cdd:smart00474 83 AKFDLHVLA-RFGIELENIFDTMLAAYLLlGGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADALL 161
|
....*..
gi 386271152 161 SLYHQMQ 167
Cdd:smart00474 162 RLYEKLE 168
|
|
| Rrp6p_like_exo |
cd06147 |
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ... |
5-173 |
6.36e-21 |
|
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: 89.19 E-value: 6.36e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 5 YLDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIAN--DDVIacIDPLAI-DDLTPLFDVLYQPKMTLVFHA 81
Cdd:cd06147 7 FVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTreEDYI--VDTLKLrDDMHILNEVFTDPNILKVFHG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 82 ARQDLELLlmhrQQlpD------TIFDTQLAASVLGLGEQvGYGNLVKTVLNVDLDKAHSRTDWTARPLSTAQLDYAADD 155
Cdd:cd06147 85 ADSDIIWL----QR--DfglyvvNLFDTGQAARVLNLPRH-SLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYARED 157
|
170
....*....|....*...
gi 386271152 156 VRYLRSLYHQMQQSLTEL 173
Cdd:cd06147 158 THYLLYIYDRLRNELLER 175
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
25-166 |
3.18e-18 |
|
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: 80.75 E-value: 3.18e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 25 LAVDTEFLREKTYYPQLCLIQIA-NDDVIACIDPLAID-DLTPLFDVLYQPKMTLVFHAARQDLELLLMHRQQLPDTIFD 102
Cdd:cd09018 2 FAFDTETDSLDNISANLVLIQLAiEPGVAALIPVAHDYlALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFD 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386271152 103 TQLAASVLG-LGEQVGYGNLVKTVLNVDLDKAHSRTD--WTARPLSTAQLDYAADDVRYLRSLYHQM 166
Cdd:cd09018 82 TMLEAYILNsVAGRWDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
213-280 |
2.61e-15 |
|
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Pssm-ID: 425755 [Multi-domain] Cd Length: 68 Bit Score: 69.87 E-value: 2.61e-15
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 386271152 213 QLANLQQLAAWRERNAIQRNRPRRWILKDDVMLDLARFAPDSLTKLSQIRGLEPRDIDRHGQAILDVL 280
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEEILAAI 68
|
|
| WRN_exo |
cd06141 |
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ... |
25-168 |
1.21e-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: 71.07 E-value: 1.21e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 25 LAVDTEF--LREKTYYPQLCLIQIANDDVIACIDPLAIDDLTP-LFDVLYQPKMTLVFHAARQDLELLLMHRQQLPDTIF 101
Cdd:cd06141 21 VGFDTEWrpSFRKGKRNKVALLQLATESRCLLFQLAHMDKLPPsLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVV 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 386271152 102 DTQ-LAASVLGLGEQVGYGNLVKTVLNVDLDK--AHSRTDWTARPLSTAQLDYAADDVrYL-RSLYHQMQQ 168
Cdd:cd06141 101 DLShLAKRVGPRRKLVSLARLVEEVLGLPLSKpkKVRCSNWEARPLSKEQILYAATDA-YAsLELYRKLLA 170
|
|
| mut-7_like_exo |
cd06146 |
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ... |
3-163 |
8.46e-09 |
|
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: 54.99 E-value: 8.46e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 3 VLYLDTPVGLLDFCQQI--QNSSWLAVDTEF--LREKTYYPQLCLIQIANDDVIACIDPLAI-----DDLTPLFDVLYQ- 72
Cdd:cd06146 1 IHIVDSEEELEALLLALslEAGRVVGIDSEWkpSFLGDSDPRVAILQLATEDEVFLLDLLALenlesEDWDRLLKRLFEd 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 73 PKMTLVFHAARQDLELL------LMHRQQLPDTIFDTQLAA-----------SVLGLGEQVGYGNLVKTVLNVDLDKAHS 135
Cdd:cd06146 81 PDVLKLGFGFKQDLKALsasypaLKCMFERVQNVLDLQNLAkelqksdmgrlKGNLPSKTKGLADLVQEVLGKPLDKSEQ 160
|
170 180
....*....|....*....|....*...
gi 386271152 136 RTDWTARPLSTAQLDYAADDVRYLRSLY 163
Cdd:cd06146 161 CSNWERRPLREEQILYAALDAYCLLEVF 188
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
6-182 |
1.85e-08 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 56.25 E-value: 1.85e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 6 LDTPVGLLDFCQQIQNSSWLAVDTEFLREKTYYPQLCLIQIANDDVIACIDPLA---IDDLTPLFDVLYQPKMTLVFHAA 82
Cdd:PRK05755 299 ILDEEELEAWLAKLKAAGLFAFDTETTSLDPMQAELVGLSFAVEPGEAAYIPLDqldREVLAALKPLLEDPAIKKVGQNL 378
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 83 RQDLELLLMHRQQLPDTIFDTQLAASVLGLGEQVGYGNLVKTVLNVDL----DKAHSRTDWTARPLSTAqLDYAADDVRY 158
Cdd:PRK05755 379 KYDLHVLARYGIELRGIAFDTMLASYLLDPGRRHGLDSLAERYLGHKTisfeEVAGKQLTFAQVDLEEA-AEYAAEDADV 457
|
170 180
....*....|....*....|....
gi 386271152 159 LRSLYHQMQQSLTELNRTHWLADD 182
Cdd:PRK05755 458 TLRLHEVLKPKLLEEPGLLELYEE 481
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
211-287 |
2.65e-08 |
|
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: 50.76 E-value: 2.65e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386271152 211 PRQLANLQQLAAWRERNAIQRNRPRRWILKDDVMLDLARFAPDSLTKLSQIRGLEPRDIDRHGQAILDVLEKASQIP 287
Cdd:smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSP 78
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
38-166 |
4.18e-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: 49.98 E-value: 4.18e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 38 YPQLCLIQIAND-------DVIACiDPLAIDDltPLFDVLYQPKMTLVFHAARQDLELLLMHRQQLPDTIFDTQLAASVL 110
Cdd:cd06148 25 KGKLCLVQIATRtgqiylfDILKL-GSIVFIN--GLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDTQVADALL 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386271152 111 GLGEQVGYgNLVKTVLNVDLDKAH--------------SRTD---WTARPLSTAQLDYAADDVRYLRSLYHQM 166
Cdd:cd06148 102 QEQETGGF-NPDRVISLVQLLDKYlyisislkedvkklMREDpkfWALRPLTEDMIRYAALDVLCLLPLYYAM 173
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
97-178 |
6.59e-05 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 44.98 E-value: 6.59e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386271152 97 PDTIFDTQLAASVLGLGEQVGYGNLVKTV---LNVDLDKAHSRTDWTArPLSTAQLDYAADDVRYLRSLYHQMQQSLTEL 173
Cdd:PRK14975 69 VERCHDLMLASQLLLGSEGRAGSSLSAAAaraLGEGLDKPPQTSALSD-PPDEEQLLYAAADADVLLELYAVLADQLNRI 147
|
....*
gi 386271152 174 NRTHW 178
Cdd:PRK14975 148 AAAAH 152
|
|
| |
