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Conserved domains on  [gi|504944244|ref|WP_015131346|]
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3'-5' exonuclease [Calothrix sp. PCC 7507]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnd super family cl33845
Ribonuclease D [Translation, ribosomal structure and biogenesis];
3-253 1.06e-51

Ribonuclease D [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG0349:

Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 173.90  E-value: 1.06e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   3 YLTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVVAefVEQIMVNPLIE 82
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLAD------GEEVALIDPLAIGDLSP--LWELLADPAIV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  83 KVFHNASYDVKFL---GSKQVKNITCTlEIAKKIpyyLLPLPNYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDY 159
Cdd:COG0349   73 KVFHAAREDLEILyhlFGILPKPLFDT-QIAAAL---LGYGDSVGYAALVEELLGVE-LDKSEQRSDWLRRPLSEEQLEY 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244 160 AYLDCIYLAQVHSQLLE-LQLKANPDPATENLTVLGTR----------YSQLEQQSK-------ILQsEFEHLQERVKKA 221
Cdd:COG0349  148 AAADVRYLLPLYEKLLEeLEREGRLEWAEEECARLLDPatyredpeeaWLRLKGAWKlnprqlaVLR-ELAAWREREARK 226

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 504944244 222 MQI---QNVSETSYCQLTSYERKTVkvafAELARL 253
Cdd:COG0349  227 RDVprnRVLKDEALLELARRQPKSL----EELARL 257
 
Name Accession Description Interval E-value
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
3-253 1.06e-51

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 173.90  E-value: 1.06e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   3 YLTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVVAefVEQIMVNPLIE 82
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLAD------GEEVALIDPLAIGDLSP--LWELLADPAIV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  83 KVFHNASYDVKFL---GSKQVKNITCTlEIAKKIpyyLLPLPNYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDY 159
Cdd:COG0349   73 KVFHAAREDLEILyhlFGILPKPLFDT-QIAAAL---LGYGDSVGYAALVEELLGVE-LDKSEQRSDWLRRPLSEEQLEY 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244 160 AYLDCIYLAQVHSQLLE-LQLKANPDPATENLTVLGTR----------YSQLEQQSK-------ILQsEFEHLQERVKKA 221
Cdd:COG0349  148 AAADVRYLLPLYEKLLEeLEREGRLEWAEEECARLLDPatyredpeeaWLRLKGAWKlnprqlaVLR-ELAAWREREARK 226

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 504944244 222 MQI---QNVSETSYCQLTSYERKTVkvafAELARL 253
Cdd:COG0349  227 RDVprnRVLKDEALLELARRQPKSL----EELARL 257
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 9-176 1.13e-38

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: 134.58  E-value: 1.13e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   9 EIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDvvAEFVEQIMVNPLIEKVFHNA 88
Cdd:cd06142    1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQIST------GGEVYLIDPLAIGD--LSPLKELLADPNIVKVFHAA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  89 SYDVKFL---GSKQVKNITCTlEIAKKIPYYLLPLpnyQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDYAYLDCI 165
Cdd:cd06142   73 REDLELLkrdFGILPQNLFDT-QIAARLLGLGDSV---GLAALVEELLGVE-LDKGEQRSDWSKRPLTDEQLEYAALDVR 147

                        170
                 ....*....|.
gi 504944244 166 YLAQVHSQLLE 176
Cdd:cd06142  148 YLLPLYEKLKE 158
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 5-177 1.79e-21

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: 89.28  E-value: 1.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    5 TSPSEIRHIIAEYTKARTLWLDTEVADYKSR--RPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVVAEFVEQIMVNPLIE 82
Cdd:pfam01612   5 TTEDELEDLIEELLNAPYVAVDTETTSLDTYsyYLRGALIQIGT------GEGAYIIDPLALGDDVLSALKRLLEDPNIT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   83 KVFHNASYDVKFL---GSKQVKNITCTlEIAKkipyYLLPLP-NYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQID 158
Cdd:pfam01612  79 KVGHNAKFDLEVLardFGIKLRNLFDT-MLAA----YLLGYDrSHSLADLAEKYLGVE-LDKEEQCSDWQARPLSEEQLR 152

                         170
                  ....*....|....*....
gi 504944244  159 YAYLDCIYLAQVHSQLLEL 177
Cdd:pfam01612 153 YAALDADYLLRLYDKLRKE 171
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 1-177 5.38e-19

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: 82.40  E-value: 5.38e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244     1 MPYLTSPSEIRHIIAEYTKART-LWLDTEVADYKSRRPRLSLIQVLDNpqdmsGDRVYLLDVLDQPDVVAEFvEQIMVNP 79
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGGeVALDTETTGLDSYSGKLVLIQISVT-----GEGAFIIDPLALGDDLEIL-KDLLEDE 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    80 LIEKVFHNASYDVKFL--GSKQVKNITCTlEIAKKipyylLPLPNYQLKTLATVLCDFNN--IDKQEQNSDWGKRPLTEE 155
Cdd:smart00474  75 TITKVGHNAKFDLHVLarFGIELENIFDT-MLAAY-----LLLGGPSKHGLATLLLGYLGveLDKEEQKSDWGARPLSEE 148

                          170       180
                   ....*....|....*....|..
gi 504944244   156 QIDYAYLDCIYLAQVHSQLLEL 177
Cdd:smart00474 149 QLEYAAEDADALLRLYEKLEKE 170
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 4-176 6.74e-13

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: 68.26  E-value: 6.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    4 LTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLdQPDVVAEFVEqIMVNPLIEK 83
Cdd:TIGR01388   2 ITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVAD------GEQLALIDPL-VIIDWSPLKE-LLRDESVVK 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   84 VFHNASYDvkflgskqvknitctLEIAKKIpYYLLPLPNYQLKTLAtVLCDFN---------------NIDKQEQNSDWG 148
Cdd:TIGR01388  74 VLHAASED---------------LEVFLNL-FGELPQPLFDTQIAA-AFCGFGmsmgyaklvqevlgvELDKSESRTDWL 136

                         170       180
                  ....*....|....*....|....*...
gi 504944244  149 KRPLTEEQIDYAYLDCIYLAQVHSQLLE 176
Cdd:TIGR01388 137 ARPLTDAQLEYAAADVTYLLPLYAKLME 164
PRK10829 PRK10829
ribonuclease D; Provisional
 4-176 4.55e-09

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 56.93  E-value: 4.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   4 LTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVvAEFVEqIMVNPLIEK 83
Cdd:PRK10829   6 ITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYD------GEQLSLIDPLGITDW-SPFKA-LLRDPQVTK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  84 VFHNASYDVK-FLGSKQVknitctleiakkipyylLPLPNYQLKTLA------------TVLCDFNNI--DKQEQNSDWG 148
Cdd:PRK10829  78 FLHAGSEDLEvFLNAFGE-----------------LPQPLIDTQILAafcgrplscgfaSMVEEYTGVtlDKSESRTDWL 140

                        170       180
                 ....*....|....*....|....*...
gi 504944244 149 KRPLTEEQIDYAYLDCIYLAQVHSQLLE 176
Cdd:PRK10829 141 ARPLSERQCEYAAADVFYLLPIAAKLMA 168
 
Name Accession Description Interval E-value
Rnd COG0349
Ribonuclease D [Translation, ribosomal structure and biogenesis];
3-253 1.06e-51

Ribonuclease D [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440118 [Multi-domain]  Cd Length: 365  Bit Score: 173.90  E-value: 1.06e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   3 YLTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVVAefVEQIMVNPLIE 82
Cdd:COG0349    1 LITTDEELAALCARLAQAPAVAVDTEFMRERTYYPRLCLIQLAD------GEEVALIDPLAIGDLSP--LWELLADPAIV 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  83 KVFHNASYDVKFL---GSKQVKNITCTlEIAKKIpyyLLPLPNYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDY 159
Cdd:COG0349   73 KVFHAAREDLEILyhlFGILPKPLFDT-QIAAAL---LGYGDSVGYAALVEELLGVE-LDKSEQRSDWLRRPLSEEQLEY 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244 160 AYLDCIYLAQVHSQLLE-LQLKANPDPATENLTVLGTR----------YSQLEQQSK-------ILQsEFEHLQERVKKA 221
Cdd:COG0349  148 AAADVRYLLPLYEKLLEeLEREGRLEWAEEECARLLDPatyredpeeaWLRLKGAWKlnprqlaVLR-ELAAWREREARK 226

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 504944244 222 MQI---QNVSETSYCQLTSYERKTVkvafAELARL 253
Cdd:COG0349  227 RDVprnRVLKDEALLELARRQPKSL----EELARL 257
RNaseD_exo cd06142
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ...
 9-176 1.13e-38

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: 134.58  E-value: 1.13e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   9 EIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDvvAEFVEQIMVNPLIEKVFHNA 88
Cdd:cd06142    1 ELEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQIST------GGEVYLIDPLAIGD--LSPLKELLADPNIVKVFHAA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  89 SYDVKFL---GSKQVKNITCTlEIAKKIPYYLLPLpnyQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDYAYLDCI 165
Cdd:cd06142   73 REDLELLkrdFGILPQNLFDT-QIAARLLGLGDSV---GLAALVEELLGVE-LDKGEQRSDWSKRPLTDEQLEYAALDVR 147

                        170
                 ....*....|.
gi 504944244 166 YLAQVHSQLLE 176
Cdd:cd06142  148 YLLPLYEKLKE 158
DNA_pol_A_exo1 pfam01612
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ...
 5-177 1.79e-21

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: 89.28  E-value: 1.79e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    5 TSPSEIRHIIAEYTKARTLWLDTEVADYKSR--RPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVVAEFVEQIMVNPLIE 82
Cdd:pfam01612   5 TTEDELEDLIEELLNAPYVAVDTETTSLDTYsyYLRGALIQIGT------GEGAYIIDPLALGDDVLSALKRLLEDPNIT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   83 KVFHNASYDVKFL---GSKQVKNITCTlEIAKkipyYLLPLP-NYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQID 158
Cdd:pfam01612  79 KVGHNAKFDLEVLardFGIKLRNLFDT-MLAA----YLLGYDrSHSLADLAEKYLGVE-LDKEEQCSDWQARPLSEEQLR 152

                         170
                  ....*....|....*....
gi 504944244  159 YAYLDCIYLAQVHSQLLEL 177
Cdd:pfam01612 153 YAALDADYLLRLYDKLRKE 171
35EXOc smart00474
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ...
 1-177 5.38e-19

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: 82.40  E-value: 5.38e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244     1 MPYLTSPSEIRHIIAEYTKART-LWLDTEVADYKSRRPRLSLIQVLDNpqdmsGDRVYLLDVLDQPDVVAEFvEQIMVNP 79
Cdd:smart00474   1 VIVVTDSETLEELLEKLRAAGGeVALDTETTGLDSYSGKLVLIQISVT-----GEGAFIIDPLALGDDLEIL-KDLLEDE 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    80 LIEKVFHNASYDVKFL--GSKQVKNITCTlEIAKKipyylLPLPNYQLKTLATVLCDFNN--IDKQEQNSDWGKRPLTEE 155
Cdd:smart00474  75 TITKVGHNAKFDLHVLarFGIELENIFDT-MLAAY-----LLLGGPSKHGLATLLLGYLGveLDKEEQKSDWGARPLSEE 148

                          170       180
                   ....*....|....*....|..
gi 504944244   156 QIDYAYLDCIYLAQVHSQLLEL 177
Cdd:smart00474 149 QLEYAAEDADALLRLYEKLEKE 170
mut-7_like_exo cd06146
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ...
 35-176 2.16e-16

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: 75.79  E-value: 2.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  35 RRPRLSLIQVldnpqdMSGDRVYLLDVL----DQPDVVAEFVEQIMVNPLIEKVFHNASYDVKFLGS---------KQVK 101
Cdd:cd06146   39 SDPRVAILQL------ATEDEVFLLDLLalenLESEDWDRLLKRLFEDPDVLKLGFGFKQDLKALSAsypalkcmfERVQ 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244 102 NITCTLEIAKK-------IPYYLLPLPNYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQIDYAYLDCIYLAQVHSQL 174
Cdd:cd06146  113 NVLDLQNLAKElqksdmgRLKGNLPSKTKGLADLVQEVLGKP-LDKSEQCSNWERRPLREEQILYAALDAYCLLEVFDKL 191


                 ..
gi 504944244 175 LE 176
Cdd:cd06146  192 LE 193
RNaseD_like cd06129
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ...
 25-174 2.09e-13

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: 66.77  E-value: 2.09e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  25 LDTEVADYKSRRPRLSLIQVLDnpqdmSGDRVYLLDVLDqpdvVAEF---VEQIMVNPLIEKVFHNASYDV-KFL--GSK 98
Cdd:cd06129   18 FDMEWPPGRRYYGEVALIQLCV-----SEEKCYLFDPLS----LSVDwqgLKMLLENPSIVKALHGIEGDLwKLLrdFGE 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504944244  99 QVKNITCTLEIAKKIpyyLLPLPNyqlkTLATVLCDFNN--IDKQEQNSDWGKRPLTEEQIDYAYLDCIYLAQVHSQL 174
Cdd:cd06129   89 KLQRLFDTTIAANLK---GLPERW----SLASLVEHFLGktLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKL 159
rnd TIGR01388
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ...
 4-176 6.74e-13

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: 68.26  E-value: 6.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244    4 LTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLdQPDVVAEFVEqIMVNPLIEK 83
Cdd:TIGR01388   2 ITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVAD------GEQLALIDPL-VIIDWSPLKE-LLRDESVVK 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   84 VFHNASYDvkflgskqvknitctLEIAKKIpYYLLPLPNYQLKTLAtVLCDFN---------------NIDKQEQNSDWG 148
Cdd:TIGR01388  74 VLHAASED---------------LEVFLNL-FGELPQPLFDTQIAA-AFCGFGmsmgyaklvqevlgvELDKSESRTDWL 136

                         170       180
                  ....*....|....*....|....*...
gi 504944244  149 KRPLTEEQIDYAYLDCIYLAQVHSQLLE 176
Cdd:TIGR01388 137 ARPLTDAQLEYAAADVTYLLPLYAKLME 164
Rrp6p_like_exo cd06147
DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen ...
 3-193 4.48e-12

DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins; Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.


Pssm-ID: 99850 [Multi-domain]  Cd Length: 192  Bit Score: 63.77  E-value: 4.48e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   3 YLTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDNPQDmsgdrvYLLDVLDQPDVVaEFVEQIMVNPLIE 82
Cdd:cd06147    7 FVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREED------YIVDTLKLRDDM-HILNEVFTDPNIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  83 KVFHNASYDVKFLgskQ------VKNITCTLEIAKkipyyLLPLPNYQLKTLATVLCDFNnIDKQEQNSDWGKRPLTEEQ 156
Cdd:cd06147   80 KVFHGADSDIIWL---QrdfglyVVNLFDTGQAAR-----VLNLPRHSLAYLLQKYCNVD-ADKKYQLADWRIRPLPEEM 150

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 504944244 157 IDYAYLDCIYLAQVHSQL-LELQLKANPDPATENLTVL 193
Cdd:cd06147  151 IKYAREDTHYLLYIYDRLrNELLERANALAPNLLESVL 188
PRK10829 PRK10829
ribonuclease D; Provisional
 4-176 4.55e-09

ribonuclease D; Provisional


Pssm-ID: 236771 [Multi-domain]  Cd Length: 373  Bit Score: 56.93  E-value: 4.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   4 LTSPSEIRHIIAEYTKARTLWLDTEVADYKSRRPRLSLIQVLDnpqdmsGDRVYLLDVLDQPDVvAEFVEqIMVNPLIEK 83
Cdd:PRK10829   6 ITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYD------GEQLSLIDPLGITDW-SPFKA-LLRDPQVTK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  84 VFHNASYDVK-FLGSKQVknitctleiakkipyylLPLPNYQLKTLA------------TVLCDFNNI--DKQEQNSDWG 148
Cdd:PRK10829  78 FLHAGSEDLEvFLNAFGE-----------------LPQPLIDTQILAafcgrplscgfaSMVEEYTGVtlDKSESRTDWL 140

                        170       180
                 ....*....|....*....|....*...
gi 504944244 149 KRPLTEEQIDYAYLDCIYLAQVHSQLLE 176
Cdd:PRK10829 141 ARPLSERQCEYAAADVFYLLPIAAKLMA 168
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 5-163 1.70e-07

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: 50.27  E-value: 1.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244   5 TSPSEIRHIIAEYTKARTLW-LDTE-VADY-KSRRPRLSLIQVldnpqdMSGDRVYLLDVLDQPDVVAEFVeQIMVNPLI 81
Cdd:cd06141    2 DSAQDAEEAVKELLGKEKVVgFDTEwRPSFrKGKRNKVALLQL------ATESRCLLFQLAHMDKLPPSLK-QLLEDPSI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  82 EKVFHNASYDVKFLGSK---QVKNItctLEIAkkipyYLLPLPNYQ-----LKTLA-TVLCDFNNIDKQEQNSDWGKRPL 152
Cdd:cd06141   75 LKVGVGIKGDARKLARDfgiEVRGV---VDLS-----HLAKRVGPRrklvsLARLVeEVLGLPLSKPKKVRCSNWEARPL 146

                        170
                 ....*....|.
gi 504944244 153 TEEQIDYAYLD 163
Cdd:cd06141  147 SKEQILYAATD 157
DEDDy_polA_RNaseD_like_exo cd09018
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ...
 25-174 1.08e-05

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: 44.54  E-value: 1.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  25 LDTEVADYKSRRPRLSLIQVLDNPQdmsgdRVYLLDVLDQpDVVAEFVEQIMVNPLIEKVFHNASYDVKFL---GSKQVK 101
Cdd:cd09018    4 FDTETDSLDNISANLVLIQLAIEPG-----VAALIPVAHD-YLALELLKPLLEDEKALKVGQNLKYDRGILlnyFIELRG 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504944244 102 NITCTLEIAKKIpyyLLPLPNYQLKTLATVLCDFNNI-DKQEQNSDWGKRPLTEEQIDYAYLDCIYLAQVHSQL 174
Cdd:cd09018   78 IAFDTMLEAYIL---NSVAGRWDMDSLVERWLGHKLIkFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
PRK06063 PRK06063
DEDDh family exonuclease;
60-129 5.83e-05

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 43.92  E-value: 5.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  60 DVL-DQP---DVVAEFVEQIMVNPLiekVFHNASYDVKFLGSKQ--------VKNITCTLEIAKKIPyylLPLPNYQLKT 127
Cdd:PRK06063  73 EMLeGQPqfaDIAGEVAELLRGRTL---VAHNVAFDYSFLAAEAeragaelpVDQVMCTVELARRLG---LGLPNLRLET 146


                 ..
gi 504944244 128 LA 129
Cdd:PRK06063 147 LA 148
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 58-139 7.81e-05

DEDDh 3'-5' exonuclease domain family; DEDDh 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. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 42.29  E-value: 7.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  58 LLDVLDQPDVVAEFVEQIMVNPLiekVFHNASYDVKFL--------GSKQVKNITCTLEIAKKipyYLLPLPNYQLKTLA 129
Cdd:cd06127   60 LADAPPFEEVLPEFLEFLGGRVL---VAHNASFDLRFLnrelrrlgGPPLPNPWIDTLRLARR---LLPGLRSHRLGLLL 133

                         90
                 ....*....|
gi 504944244 130 TVLCDFNNID 139
Cdd:cd06127  134 AERYGIPLEG 143
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 60-139 3.70e-04

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 40.16  E-value: 3.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  60 DVLDQP---DVVAEFVEQIMVNPLiekVFHNASYDVKFLGS--------KQVKNITCTLEIAKKipyyLLP-LPNYQLKT 127
Cdd:COG0847   60 DVADAPpfaEVLPELLEFLGGAVL---VAHNAAFDLGFLNAelrraglpLPPFPVLDTLRLARR----LLPgLPSYSLDA 132

                         90
                 ....*....|..
gi 504944244 128 latvLCDFNNID 139
Cdd:COG0847  133 ----LCERLGIP 140
PRK06807 PRK06807
3'-5' exonuclease;
61-173 8.14e-04

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 40.57  E-value: 8.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  61 VLDQP---DVVAEFVEQIMVNPLiekVFHNASYDVKFLGS-------KQVKN-ITCTLEIAKKipyYLLPLPNYQLKTLA 129
Cdd:PRK06807  69 VSDAPtieEVLPLFLAFLHTNVI---VAHNASFDMRFLKSnvnmlglPEPKNkVIDTVFLAKK---YMKHAPNHKLETLK 142

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 504944244 130 TVLCdfnnIDKQEQNsdwgkrplteeqidyAYLDCIYLAQVHSQ 173
Cdd:PRK06807 143 RMLG----IRLSSHN---------------AFDDCITCAAVYQK 167
Egl_like_exo cd06148
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ...
 140-176 1.50e-03

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: 38.80  E-value: 1.50e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 504944244 140 KQEQNSDWGKRPLTEEQIDYAYLDCIYLAQVHSQLLE 176
Cdd:cd06148  139 MREDPKFWALRPLTEDMIRYAALDVLCLLPLYYAMLD 175
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 47-112 2.69e-03

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 37.90  E-value: 2.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504944244  47 NPQ-DMSGD--RVYLL---DVLDQP---DVVAEFVEQIMVNPLiekVFHNASYDVKFLGS-----------KQVKNITCT 106
Cdd:cd06131   42 NPErDIPEEafKVHGItdeFLADKPkfaEIADEFLDFIRGAEL---VIHNASFDVGFLNAelsllglgkkiIDFCRVIDT 118


                 ....*.
gi 504944244 107 LEIAKK 112
Cdd:cd06131  119 LALARK 124
 
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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