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Conserved domains on  [gi|767904671|ref|XP_005263532|]
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exosome complex component 10 isoform X1 [Homo sapiens]

Protein Classification

3'-5' exonuclease family protein; RRP6 family protein( domain architecture ID 10547357)

3'-5' exonuclease family protein similar to Trypanosoma brucei Rrp6p homologue that is part of the exosome complex which is involved in 3'-processing of many RNA species; RRP6 family protein may be involved in the degradation of aberrant transcripts and processing of precursors to stable RNAs

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
284-474 2.23e-130

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: 388.49  E-value: 2.23e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 284 EETPCHFISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVK 363
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 364 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHY 443
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160
                        170       180       190
                 ....*....|....*....|....*....|..
gi 767904671 444 LLYIYDKMRLEMWERGN-GQPVQLQVVWQRSR 474
Cdd:cd06147  161 LLYIYDRLRNELLERANaLAPNLLESVLNCSR 192
PMC2NT pfam08066
PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC ...
44-133 5.09e-29

PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.


:

Pssm-ID: 462352  Cd Length: 89  Bit Score: 111.12  E-value: 5.09e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   44 VAVTKASGGLPqfGDEYDFYRSF-PGFQAFCETQGDRLLQCMSRVMQYHGCRSNIKDRSKVTELEDKFDLLVDANDVILE 122
Cdd:pfam08066   1 VSTTRAANALP--AQDIDFYRSLdPEFAESLDEQSARLLSLINSLLQSAGSKSNIKAPGDLDDVEDRWDSVVDVNDSLLE 78
                          90
                  ....*....|.
gi 767904671  123 RVGILLDEASG 133
Cdd:pfam08066  79 KADICLDELTG 89
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
503-583 7.37e-22

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: 90.43  E-value: 7.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   503 NTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPLL 582
Cdd:smart00341   1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPSE 80

                   .
gi 767904671   583 K 583
Cdd:smart00341  81 A 81
 
Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
284-474 2.23e-130

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: 388.49  E-value: 2.23e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 284 EETPCHFISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVK 363
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 364 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHY 443
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160
                        170       180       190
                 ....*....|....*....|....*....|..
gi 767904671 444 LLYIYDKMRLEMWERGN-GQPVQLQVVWQRSR 474
Cdd:cd06147  161 LLYIYDRLRNELLERANaLAPNLLESVLNCSR 192
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
288-456 2.77e-63

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: 210.62  E-value: 2.77e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  288 CHFISSLDELVELNEKLLNCQEFAVDLEHHSYR--SFLGLTCLMQISTRTEDFIIDTLELRSD-MYILNESLTDPAIVKV 364
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDDvLSALKRLLEDPNITKV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  365 FHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGR-HSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHY 443
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160
                         170
                  ....*....|...
gi 767904671  444 LLYIYDKMRLEMW 456
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
290-606 8.18e-56

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 197.02  E-value: 8.18e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 290 FISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELrSDMYILNESLTDPAIVKVFHGAD 369
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAI-GDLSPLWELLADPAIVKVFHAAR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 370 SDIEWLQKDFGLYVVNMFDTHQAARLLNLG-RHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIY 448
Cdd:COG0349   80 EDLEILYHLFGILPKPLFDTQIAAALLGYGdSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLY 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 449 DKMRLEMWERGNGQPVQLqvvwqrsrdiCLKKFIKPIFTDESYLELYR--KQKKHLNTQQLTAFQLLFAWRDKTARREDE 526
Cdd:COG0349  160 EKLLEELEREGRLEWAEE----------ECARLLDPATYREDPEEAWLrlKGAWKLNPRQLAVLRELAAWREREARKRDV 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 527 SYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPllKSEVAAGVKKSGPLPSAERLENVL 606
Cdd:COG0349  230 PRNRVLKDEALLELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALP--EEELPEPPRRLPLSPGYKALLKLL 307
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
289-456 7.55e-46

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: 162.14  E-value: 7.55e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   289 HFISSLDELVELNEKL-LNCQEFAVDLEHHSYRSFLGLTCLMQIS-TRTEDFIIDTLELRSDMYILNESLTDPAIVKVFH 366
Cdd:smart00474   2 IVVTDSETLEELLEKLrAAGGEVALDTETTGLDSYSGKLVLIQISvTGEGAFIIDPLALGDDLEILKDLLEDETITKVGH 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   367 GADSDIEWLQKdFGLYVVNMFDTHQAARLL--NLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYL 444
Cdd:smart00474  82 NAKFDLHVLAR-FGIELENIFDTMLAAYLLlgGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADAL 160
                          170
                   ....*....|..
gi 767904671   445 LYIYDKMRLEMW 456
Cdd:smart00474 161 LRLYEKLEKELE 172
PMC2NT pfam08066
PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC ...
44-133 5.09e-29

PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.


Pssm-ID: 462352  Cd Length: 89  Bit Score: 111.12  E-value: 5.09e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   44 VAVTKASGGLPqfGDEYDFYRSF-PGFQAFCETQGDRLLQCMSRVMQYHGCRSNIKDRSKVTELEDKFDLLVDANDVILE 122
Cdd:pfam08066   1 VSTTRAANALP--AQDIDFYRSLdPEFAESLDEQSARLLSLINSLLQSAGSKSNIKAPGDLDDVEDRWDSVVDVNDSLLE 78
                          90
                  ....*....|.
gi 767904671  123 RVGILLDEASG 133
Cdd:pfam08066  79 KADICLDELTG 89
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
291-580 1.68e-28

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: 118.33  E-value: 1.68e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  291 ISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELrSDMYILNESLTDPAIVKVFHGADS 370
Cdd:TIGR01388   2 ITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVI-IDWSPLKELLRDESVVKVLHAASE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  371 DIEWLQKDFGLYVVNMFDTHQAARLLNLGrHSL--DHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIY 448
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFG-MSMgyAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLY 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  449 DKMRLEMWERGNGQPVQLQVVWQRSRdicLKKFIKPiftDESYLELYRKQKkhLNTQQLTAFQLLFAWRDKTARREDESY 528
Cdd:TIGR01388 160 AKLMERLEESGRLAWLEEECTLLTDR---RTYVVNP---EDAWRDIKNAWQ--LRPQQLAVLQALAAWREREARERDLPR 231
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767904671  529 GYVLPNHMMLKIAEELPKEPqGIIACCNPVPPLVRQQINEMHLLIQQAREMP 580
Cdd:TIGR01388 232 NFVLKEEALWELARQAPGNL-TELASLGPKGSEIRKHGDTLLALVKTALALP 282
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
503-583 7.37e-22

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: 90.43  E-value: 7.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   503 NTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPLL 582
Cdd:smart00341   1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPSE 80

                   .
gi 767904671   583 K 583
Cdd:smart00341  81 A 81
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
506-573 2.26e-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: 68.33  E-value: 2.26e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767904671  506 QLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLI 573
Cdd:pfam00570   1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEEILAAI 68
PRK10829 PRK10829
ribonuclease D; Provisional
290-545 5.99e-14

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 74.65  E-value: 5.99e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 290 FISSLDELVELNEKLLNCQEFAVDLEHHSYRSF---LGLTCLM---QIStrtedfIIDTLELrSDMYILNESLTDPAIVK 363
Cdd:PRK10829   5 MITTDDALASVCEAARAFPAIALDTEFVRTRTYypqLGLIQLYdgeQLS------LIDPLGI-TDWSPFKALLRDPQVTK 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 364 VFHGADSDIEWLQKDFGLYVVNMFDTHQAA----RLLNLGRHSLdhlLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARD 439
Cdd:PRK10829  78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAafcgRPLSCGFASM---VEEYTGVTLDKSESRTDWLARPLSERQCEYAAA 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 440 DTHYLLYIYDKMRLEMWERGngqpvQLQVVWQRSRDICLKKfiKPIFTDEsylELYRK--QKKHLNTQQLTAFQLLFAWR 517
Cdd:PRK10829 155 DVFYLLPIAAKLMAETEAAG-----WLPAALDECRLLCQRR--QEVLAPE---EAYRDitNAWQLRTRQLACLQLLADWR 224
                        250       260
                 ....*....|....*....|....*...
gi 767904671 518 DKTARREDESYGYVLPNHMMLKIAEELP 545
Cdd:PRK10829 225 LRKARERDLAVNFVVREEHLWQVARYMP 252
 
Name Accession Description Interval E-value
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
284-474 2.23e-130

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: 388.49  E-value: 2.23e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 284 EETPCHFISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVK 363
Cdd:cd06147    1 DETPLTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREEDYIVDTLKLRDDMHILNEVFTDPNILK 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 364 VFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHY 443
Cdd:cd06147   81 VFHGADSDIIWLQRDFGLYVVNLFDTGQAARVLNLPRHSLAYLLQKYCNVDADKKYQLADWRIRPLPEEMIKYAREDTHY 160
                        170       180       190
                 ....*....|....*....|....*....|..
gi 767904671 444 LLYIYDKMRLEMWERGN-GQPVQLQVVWQRSR 474
Cdd:cd06147  161 LLYIYDRLRNELLERANaLAPNLLESVLNCSR 192
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
288-456 2.77e-63

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: 210.62  E-value: 2.77e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  288 CHFISSLDELVELNEKLLNCQEFAVDLEHHSYR--SFLGLTCLMQISTRTEDFIIDTLELRSD-MYILNESLTDPAIVKV 364
Cdd:pfam01612   1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDtySYYLRGALIQIGTGEGAYIIDPLALGDDvLSALKRLLEDPNITKV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  365 FHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNLGR-HSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHY 443
Cdd:pfam01612  81 GHNAKFDLEVLARDFGIKLRNLFDTMLAAYLLGYDRsHSLADLAEKYLGVELDKEEQCSDWQARPLSEEQLRYAALDADY 160
                         170
                  ....*....|...
gi 767904671  444 LLYIYDKMRLEMW 456
Cdd:pfam01612 161 LLRLYDKLRKELE 173
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
290-606 8.18e-56

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 197.02  E-value: 8.18e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 290 FISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELrSDMYILNESLTDPAIVKVFHGAD 369
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLADGEEVALIDPLAI-GDLSPLWELLADPAIVKVFHAAR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 370 SDIEWLQKDFGLYVVNMFDTHQAARLLNLG-RHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIY 448
Cdd:COG0349   80 EDLEILYHLFGILPKPLFDTQIAAALLGYGdSVGYAALVEELLGVELDKSEQRSDWLRRPLSEEQLEYAAADVRYLLPLY 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 449 DKMRLEMWERGNGQPVQLqvvwqrsrdiCLKKFIKPIFTDESYLELYR--KQKKHLNTQQLTAFQLLFAWRDKTARREDE 526
Cdd:COG0349  160 EKLLEELEREGRLEWAEE----------ECARLLDPATYREDPEEAWLrlKGAWKLNPRQLAVLRELAAWREREARKRDV 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 527 SYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPllKSEVAAGVKKSGPLPSAERLENVL 606
Cdd:COG0349  230 PRNRVLKDEALLELARRQPKSLEELARLRGLSPGEIRRHGEELLAAVAEALALP--EEELPEPPRRLPLSPGYKALLKLL 307
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
296-454 8.42e-56

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: 190.05  E-value: 8.42e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 296 ELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELrSDMYILNESLTDPAIVKVFHGADSDIEWL 375
Cdd:cd06142    1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTGGEVYLIDPLAI-GDLSPLKELLADPNIVKVFHAAREDLELL 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 376 QKDFGLYVVNMFDTHQAARLLNLG-RHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMRLE 454
Cdd:cd06142   80 KRDFGILPQNLFDTQIAARLLGLGdSVGLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLKEE 159
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
309-452 3.76e-47

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: 165.38  E-value: 3.76e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 309 EFAVDLEHHSYRSFLGLTCLMQISTRTE-DFIIDTLELRSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMF 387
Cdd:cd06129   15 VIAFDMEWPPGRRYYGEVALIQLCVSEEkCYLFDPLSLSVDWQGLKMLLENPSIVKALHGIEGDLWKLLRDFGEKLQRLF 94
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904671 388 DTHQAARLLNL-GRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMR 452
Cdd:cd06129   95 DTTIAANLKGLpERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLR 160
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
289-456 7.55e-46

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: 162.14  E-value: 7.55e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   289 HFISSLDELVELNEKL-LNCQEFAVDLEHHSYRSFLGLTCLMQIS-TRTEDFIIDTLELRSDMYILNESLTDPAIVKVFH 366
Cdd:smart00474   2 IVVTDSETLEELLEKLrAAGGEVALDTETTGLDSYSGKLVLIQISvTGEGAFIIDPLALGDDLEILKDLLEDETITKVGH 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   367 GADSDIEWLQKdFGLYVVNMFDTHQAARLL--NLGRHSLDHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYL 444
Cdd:smart00474  82 NAKFDLHVLAR-FGIELENIFDTMLAAYLLlgGPSKHGLATLLLGYLGVELDKEEQKSDWGARPLSEEQLEYAAEDADAL 160
                          170
                   ....*....|..
gi 767904671   445 LYIYDKMRLEMW 456
Cdd:smart00474 161 LRLYEKLEKELE 172
PMC2NT pfam08066
PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC ...
44-133 5.09e-29

PMC2NT (NUC016) domain; This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components.


Pssm-ID: 462352  Cd Length: 89  Bit Score: 111.12  E-value: 5.09e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   44 VAVTKASGGLPqfGDEYDFYRSF-PGFQAFCETQGDRLLQCMSRVMQYHGCRSNIKDRSKVTELEDKFDLLVDANDVILE 122
Cdd:pfam08066   1 VSTTRAANALP--AQDIDFYRSLdPEFAESLDEQSARLLSLINSLLQSAGSKSNIKAPGDLDDVEDRWDSVVDVNDSLLE 78
                          90
                  ....*....|.
gi 767904671  123 RVGILLDEASG 133
Cdd:pfam08066  79 KADICLDELTG 89
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
291-580 1.68e-28

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: 118.33  E-value: 1.68e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  291 ISSLDELVELNEKLLNCQEFAVDLEHHSYRSFLGLTCLMQISTRTEDFIIDTLELrSDMYILNESLTDPAIVKVFHGADS 370
Cdd:TIGR01388   2 ITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADGEQLALIDPLVI-IDWSPLKELLRDESVVKVLHAASE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  371 DIEWLQKDFGLYVVNMFDTHQAARLLNLGrHSL--DHLLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIY 448
Cdd:TIGR01388  81 DLEVFLNLFGELPQPLFDTQIAAAFCGFG-MSMgyAKLVQEVLGVELDKSESRTDWLARPLTDAQLEYAAADVTYLLPLY 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671  449 DKMRLEMWERGNGQPVQLQVVWQRSRdicLKKFIKPiftDESYLELYRKQKkhLNTQQLTAFQLLFAWRDKTARREDESY 528
Cdd:TIGR01388 160 AKLMERLEESGRLAWLEEECTLLTDR---RTYVVNP---EDAWRDIKNAWQ--LRPQQLAVLQALAAWREREARERDLPR 231
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767904671  529 GYVLPNHMMLKIAEELPKEPqGIIACCNPVPPLVRQQINEMHLLIQQAREMP 580
Cdd:TIGR01388 232 NFVLKEEALWELARQAPGNL-TELASLGPKGSEIRKHGDTLLALVKTALALP 282
HRDC smart00341
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ...
503-583 7.37e-22

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: 90.43  E-value: 7.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671   503 NTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLIQQAREMPLL 582
Cdd:smart00341   1 RERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKDLLAVIQEASDSPSE 80

                   .
gi 767904671   583 K 583
Cdd:smart00341  81 A 81
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
327-472 2.68e-17

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: 81.18  E-value: 2.68e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 327 CLMQISTRTED-FIIDTLEL--RSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDThQAARLLNLGRH-- 401
Cdd:cd06148   29 CLVQIATRTGQiYLFDILKLgsIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIKLNNVFDT-QVADALLQEQEtg 107
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 402 --------SLDHLLKLY-----CNVDSNKQYQLAD---WRIRPLPEEMLSYARDDTHYLLYIYDKMRLEMwergngQPVQ 465
Cdd:cd06148  108 gfnpdrviSLVQLLDKYlyisiSLKEDVKKLMREDpkfWALRPLTEDMIRYAALDVLCLLPLYYAMLDAL------ISKF 181

                 ....*..
gi 767904671 466 LQVVWQR 472
Cdd:cd06148  182 LKAVFKY 188
HRDC pfam00570
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ...
506-573 2.26e-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: 68.33  E-value: 2.26e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767904671  506 QLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEPQGIIACCNPVPPLVRQQINEMHLLI 573
Cdd:pfam00570   1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEEILAAI 68
PRK10829 PRK10829
ribonuclease D; Provisional
290-545 5.99e-14

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 74.65  E-value: 5.99e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 290 FISSLDELVELNEKLLNCQEFAVDLEHHSYRSF---LGLTCLM---QIStrtedfIIDTLELrSDMYILNESLTDPAIVK 363
Cdd:PRK10829   5 MITTDDALASVCEAARAFPAIALDTEFVRTRTYypqLGLIQLYdgeQLS------LIDPLGI-TDWSPFKALLRDPQVTK 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 364 VFHGADSDIEWLQKDFGLYVVNMFDTHQAA----RLLNLGRHSLdhlLKLYCNVDSNKQYQLADWRIRPLPEEMLSYARD 439
Cdd:PRK10829  78 FLHAGSEDLEVFLNAFGELPQPLIDTQILAafcgRPLSCGFASM---VEEYTGVTLDKSESRTDWLARPLSERQCEYAAA 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 440 DTHYLLYIYDKMRLEMWERGngqpvQLQVVWQRSRDICLKKfiKPIFTDEsylELYRK--QKKHLNTQQLTAFQLLFAWR 517
Cdd:PRK10829 155 DVFYLLPIAAKLMAETEAAG-----WLPAALDECRLLCQRR--QEVLAPE---EAYRDitNAWQLRTRQLACLQLLADWR 224
                        250       260
                 ....*....|....*....|....*...
gi 767904671 518 DKTARREDESYGYVLPNHMMLKIAEELP 545
Cdd:PRK10829 225 LRKARERDLAVNFVVREEHLWQVARYMP 252
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
288-450 2.76e-12

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: 66.55  E-value: 2.76e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 288 CHFISSLDELVELNEK--LLNCQEFAVDLE---HHSYRSFLGLtCLMQISTRTEDFIIDTLEL---RSDMYI--LNESLT 357
Cdd:cd06146    1 IHIVDSEEELEALLLAlsLEAGRVVGIDSEwkpSFLGDSDPRV-AILQLATEDEVFLLDLLALenlESEDWDrlLKRLFE 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 358 DPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTHQAARLLNL------------------GRHSLDHLLKLYCNVDSNKQY 419
Cdd:cd06146   80 DPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLakelqksdmgrlkgnlpsKTKGLADLVQEVLGKPLDKSE 159
                        170       180       190
                 ....*....|....*....|....*....|.
gi 767904671 420 QLADWRIRPLPEEMLSYARDDTHYLLYIYDK 450
Cdd:cd06146  160 QCSNWERRPLREEQILYAALDAYCLLEVFDK 190
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
310-451 1.17e-11

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: 63.41  E-value: 1.17e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 310 FAVDLEHHSYRSFLGLTCLMQISTRTED-FIIDTLELRSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFD 388
Cdd:cd09018    2 FAFDTETDSLDNISANLVLIQLAIEPGVaALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGIAFD 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767904671 389 THQAARLLN--LGRHSLDHLLKLYCNVDSNKQYQLAD--WRIRPLPEEMLSYARDDTHYLLYIYDKM 451
Cdd:cd09018   82 TMLEAYILNsvAGRWDMDSLVERWLGHKLIKFESIAGklWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
313-452 4.09e-11

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: 62.60  E-value: 4.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 313 DLEH-HSYRSFL-GLTCLMQISTRTEDFIIDTLELRSDMYILNESLTDPAIVKVFHGADSDIEWLQKDFGLYVVNMFDTH 390
Cdd:cd06141   24 DTEWrPSFRKGKrNKVALLQLATESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLS 103
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767904671 391 QAARLLNLGRH--SLDHLLKLYCNV--DSNKQYQLADWRIRPLPEEMLSYARDDTHYLLYIYDKMR 452
Cdd:cd06141  104 HLAKRVGPRRKlvSLARLVEEVLGLplSKPKKVRCSNWEARPLSKEQILYAATDAYASLELYRKLL 169
PRK05755 PRK05755
DNA polymerase I; Provisional
230-457 9.12e-06

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 49.71  E-value: 9.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 230 DLDVPPALADFIHQQrtQQVEQ--DMFAhpyQYELNHFtpadavLQKPQPQLYRPIEETPCHFISSLDELVELNEKLLNC 307
Cdd:PRK05755 247 DVPLEVDLEDLELQP--PDREKliALFK---ELEFKSL------LRRAAAAEAAPLDEEDYETILDEEELEAWLAKLKAA 315
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 308 QEFAVDLEHHSYRSFLGltCLMQISTRTED---FIIDTLELRSDMY-ILNESLTDPAIVKVFHGADSDIEWLqKDFGLYV 383
Cdd:PRK05755 316 GLFAFDTETTSLDPMQA--ELVGLSFAVEPgeaAYIPLDQLDREVLaALKPLLEDPAIKKVGQNLKYDLHVL-ARYGIEL 392
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767904671 384 VNM-FDTHQAARLLNLGR-HSLDHLLKLYCNVDS-------NKQYQLADwrirPLPEEMLSYARDDTHYLLYIYDKMRLE 454
Cdd:PRK05755 393 RGIaFDTMLASYLLDPGRrHGLDSLAERYLGHKTisfeevaGKQLTFAQ----VDLEEAAEYAAEDADVTLRLHEVLKPK 468

                 ...
gi 767904671 455 MWE 457
Cdd:PRK05755 469 LLE 471
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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