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Conserved domains on  [gi|115532678|ref|NP_001040854|]
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Putative RNA exonuclease pqe-1 [Caenorhabditis elegans]

Protein Classification

3'-5' exonuclease( domain architecture ID 11067230)

3'-5' exonuclease catalyzes the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction; similar to Pan troglodytes exonuclease GOR; belongs to the DnaQ-like (or DEDD) 3'-5' exonuclease superfamily

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 504-654 3.45e-71

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


:

Pssm-ID: 99848  Cd Length: 150  Bit Score: 227.37  E-value: 3.45e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 504 YALDCEMVYTIAGPALARLTMVDMQRNRVLDVFVKPPTDVLDPNTEFSGLTMEQINSAPDTLKTCHQKLFKYVNADTILI 583
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115532678 584 GHSLESDLKAMRVVHKNVIDTAILFRSTRD--TKVALKVLSAKLLHKNIQgdnEDAIGHDSMEDALTCVDLIF 654
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQ---QGEGGHDSVEDARAALELVK 150
EloA-BP1 super family cl24445
ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically ...
 243-389 3.25e-05

ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically between 144 and 167 amino acids in length.


The actual alignment was detected with superfamily member pfam15870:

Pssm-ID: 464914  Cd Length: 163  Bit Score: 44.67  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  243 PKILDFSVGRTFTAIRQTAIKLVFDTFLE-RDSPNAARE-AQEFELSIAKQYTDGQKYR---INIGHKvaaLRKE----- 312
Cdd:pfam15870   2 PVIPTEFGSKVPTNIRQRYLNLFIDECLKiCTSEQEAFErALEEEKAVYDRCSSKNIYLnvaVNTLKK---LRKEvpsqs 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  313 ---NTSGILEVNKNAVSHDKILAG--GPKDNCTVARGRKTHVDhrQLSIEKLHPLLLQFKLTTSELETNAYPMRR-DGST 386
Cdd:pfam15870  79 savTKSSAISSNNKVVSHEAVLGGklAAKTSFSINRNSKSIEE--DLKGATLYRMLKEYLLTEEQLKENGYPRPHpDKPG 156


                  ...
gi 115532678  387 KAV 389
Cdd:pfam15870 157 RAV 159
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 504-654 3.45e-71

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 227.37  E-value: 3.45e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 504 YALDCEMVYTIAGPALARLTMVDMQRNRVLDVFVKPPTDVLDPNTEFSGLTMEQINSAPDTLKTCHQKLFKYVNADTILI 583
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115532678 584 GHSLESDLKAMRVVHKNVIDTAILFRSTRD--TKVALKVLSAKLLHKNIQgdnEDAIGHDSMEDALTCVDLIF 654
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQ---QGEGGHDSVEDARAALELVK 150
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 502-661 2.25e-31

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 120.10  E-value: 2.25e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678   502 RVYALDCEMVYTIAGPA-LARLTMVDMQRNR---VLDVFVKPPTDVLDPNTEFSGLTMEQINSAPdTLKTCHQKLFKYVN 577
Cdd:smart00479   1 TLVVIDCETTGLDPGKDeIIEIAAVDVDGGEiieVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678   578 ADTILIGHSLESDLKAMRVVHKN----------VIDTAILFRSTRD--TKVALKVLSAKLLHKNIQGdnedaiGHDSMED 645
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPRlgikqppklpVIDTLKLARATNPglPKYSLKKLAKRLLLEVIQR------AHRALDD 153

                          170
                   ....*....|....*.
gi 115532678   646 ALTCVDLIFYGLRNPE 661
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 502-652 3.82e-06

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 47.48  E-value: 3.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 502 RVYALDCEMvyTIAGPALARLT---MVDMQRNRVLDVF---VKPPTDVLDPNTEFSGLTMEQINSAPdTLKTCHQKLFKY 575
Cdd:COG0847    1 RFVVLDTET--TGLDPAKDRIIeigAVKVDDGRIVETFhtlVNPERPIPPEATAIHGITDEDVADAP-PFAEVLPELLEF 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 576 VnADTILIGHSLESDLKAMR---------VVHKNVIDTAILFRSTRDTKVALKvLSAKLLHKNIqgDNEDAigHDSMEDA 646
Cdd:COG0847   78 L-GGAVLVAHNAAFDLGFLNaelrraglpLPPFPVLDTLRLARRLLPGLPSYS-LDALCERLGI--PFDER--HRALADA 151


                 ....*.
gi 115532678 647 LTCVDL 652
Cdd:COG0847  152 EATAEL 157
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 505-652 2.33e-05

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 45.03  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  505 ALDCEMVYTIAGP----ALARLTmVDMQRNRVLDVFVKPPTDVLDPN-----TEFSGLTMEQINSAPdTLKTCHQKLFKY 575
Cdd:pfam00929   2 VIDLETTGLDPEKdeiiEIAAVV-IDGGENEIGETFHTYVKPTRLPKltdecTKFTGITQAMLDNKP-SFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  576 VNADTILIGHSLESDLK----AMRVVHKN-------VIDTAILFRSTRdTKVALKVLsAKLLHKniQGDNEDAIGHDSME 644
Cdd:pfam00929  80 LRKGNLLVAHNASFDVGflryDDKRFLKKpmpklnpVIDTLILDKATY-KELPGRSL-DALAEK--LGLEHIGRAHRALD 155


                  ....*...
gi 115532678  645 DALTCVDL 652
Cdd:pfam00929 156 DARATAKL 163
EloA-BP1 pfam15870
ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically ...
 243-389 3.25e-05

ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically between 144 and 167 amino acids in length.


Pssm-ID: 464914  Cd Length: 163  Bit Score: 44.67  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  243 PKILDFSVGRTFTAIRQTAIKLVFDTFLE-RDSPNAARE-AQEFELSIAKQYTDGQKYR---INIGHKvaaLRKE----- 312
Cdd:pfam15870   2 PVIPTEFGSKVPTNIRQRYLNLFIDECLKiCTSEQEAFErALEEEKAVYDRCSSKNIYLnvaVNTLKK---LRKEvpsqs 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  313 ---NTSGILEVNKNAVSHDKILAG--GPKDNCTVARGRKTHVDhrQLSIEKLHPLLLQFKLTTSELETNAYPMRR-DGST 386
Cdd:pfam15870  79 savTKSSAISSNNKVVSHEAVLGGklAAKTSFSINRNSKSIEE--DLKGATLYRMLKEYLLTEEQLKENGYPRPHpDKPG 156


                  ...
gi 115532678  387 KAV 389
Cdd:pfam15870 157 RAV 159
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 504-654 3.45e-71

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 227.37  E-value: 3.45e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 504 YALDCEMVYTIAGPALARLTMVDMQRNRVLDVFVKPPTDVLDPNTEFSGLTMEQINSAPDTLKTCHQKLFKYVNADTILI 583
Cdd:cd06145    1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTILV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 115532678 584 GHSLESDLKAMRVVHKNVIDTAILFRSTRD--TKVALKVLSAKLLHKNIQgdnEDAIGHDSMEDALTCVDLIF 654
Cdd:cd06145   81 GHSLENDLKALKLIHPRVIDTAILFPHPRGppYKPSLKNLAKKYLGRDIQ---QGEGGHDSVEDARAALELVK 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 504-653 3.64e-38

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 138.95  E-value: 3.64e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 504 YALDCEMVYTIAGPA-LARLTMVDMQRNRVL-DVFVKPPTDVLDPNTEFSGLT---MEQINSAPDTL-KTCHQK--LFKY 575
Cdd:cd06137    1 VALDCEMVGLADGDSeVVRISAVDVLTGEVLiDSLVRPSVRVTDWRTRFSGVTpadLEEAAKAGKTIfGWEAARaaLWKF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 576 VNADTILIGHSLESDLKAMRVVHKNVIDTAILFRSTR-----DTKVALKVLSAKLLHKNIQGDNEdaiGHDSMEDALTCV 650
Cdd:cd06137   81 IDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVkgplaKRQWSLRTLCRDFLGLKIQGGGE---GHDSLEDALAAR 157


                 ...
gi 115532678 651 DLI 653
Cdd:cd06137  158 EVV 160
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 502-661 2.25e-31

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 120.10  E-value: 2.25e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678   502 RVYALDCEMVYTIAGPA-LARLTMVDMQRNR---VLDVFVKPPTDVLDPNTEFSGLTMEQINSAPdTLKTCHQKLFKYVN 577
Cdd:smart00479   1 TLVVIDCETTGLDPGKDeIIEIAAVDVDGGEiieVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFLR 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678   578 ADTILIGHSLESDLKAMRVVHKN----------VIDTAILFRSTRD--TKVALKVLSAKLLHKNIQGdnedaiGHDSMED 645
Cdd:smart00479  80 GRILVAGNSAHFDLRFLKLEHPRlgikqppklpVIDTLKLARATNPglPKYSLKKLAKRLLLEVIQR------AHRALDD 153

                          170
                   ....*....|....*.
gi 115532678   646 ALTCVDLIFYGLRNPE 661
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 505-646 2.41e-23

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing 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. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 96.43  E-value: 2.41e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 505 ALDCEMVYTiaGP-----ALARLTMVDMQRNRVLDVFVKPPTDVLDPNTEFSGLTMEQINSAPDtLKTCHQKLFKYVNaD 579
Cdd:cd06144    2 ALDCEMVGV--GPdgsesALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPD-FEEVQKKVAELLK-G 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 115532678 580 TILIGHSLESDLKAMRVVH--KNVIDTA--ILFRST-RDTKVALKVLSAKLLHKNIQgdnEDAigHDSMEDA 646
Cdd:cd06144   78 RILVGHALKNDLKVLKLDHpkKLIRDTSkyKPLRKTaKGKSPSLKKLAKQLLGLDIQ---EGE--HSSVEDA 144
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 518-652 8.83e-19

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with 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.


Pssm-ID: 99846  Cd Length: 174  Bit Score: 84.21  E-value: 8.83e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 518 ALARLTMVDMQRNR----VLDVFVKPPTDVLDPNTEFSGLT---MEQINS--APDTLKTCHQKLFKYVNADTILIGHSLE 588
Cdd:cd06143   32 SLARVSVVRGEGELegvpFIDDYISTTEPVVDYLTRFSGIKpgdLDPKTSskNLTTLKSAYLKLRLLVDLGCIFVGHGLA 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 115532678 589 SDLKA--MRVVHKNVIDTAILFRSTRDTKVALKVLSAKLLHKNIQGDNedaigHDSMEDALTCVDL 652
Cdd:cd06143  112 KDFRVinIQVPKEQVIDTVELFHLPGQRKLSLRFLAWYLLGEKIQSET-----HDSIEDARTALKL 172
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 505-652 7.68e-18

DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins; Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing 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. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response.


Pssm-ID: 99852  Cd Length: 157  Bit Score: 80.94  E-value: 7.68e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 505 ALDCEMVYTiaGP-----ALARLTMVDMQRNRVLDVFVKPPTDVLDPNTEFSGLTMEQ-INSAPdtLKTCHQKLFKYVNA 578
Cdd:cd06149    2 AIDCEMVGT--GPggresELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHlVNATP--FAVAQKEILKILKG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 579 dTILIGHSLESDLKAMRVVHKNVIdtailfrsTRDT----------------KVALKVLSAKLLHKNIQGDNEdaiGHDS 642
Cdd:cd06149   78 -KVVVGHAIHNDFKALKYFHPKHM--------TRDTstipllnrkagfpencRVSLKVLAKRLLHRDIQVGRQ---GHSS 145

                        170
                 ....*....|
gi 115532678 643 MEDALTCVDL 652
Cdd:cd06149  146 VEDARATMEL 155
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 505-652 9.43e-07

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: 49.22  E-value: 9.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 505 ALDCEMvyTIAGPALARLT---MVDMQRNRVL----DVFVKPPTDVLDPNTEFSGLTMEQINSAPdTLKTCHQKLFKYVn 577
Cdd:cd06127    2 VFDTET--TGLDPKKDRIIeigAVKVDGGIEIverfETLVNPGRPIPPEATAIHGITDEMLADAP-PFEEVLPEFLEFL- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 578 ADTILIGHSLESDLKAMR---------VVHKNVIDTAILFRSTRDTKVALKVLSAKLLHKNIqgDNEDAigHDSMEDALT 648
Cdd:cd06127   78 GGRVLVAHNASFDLRFLNrelrrlggpPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGI--PLEGA--HRALADALA 153


                 ....
gi 115532678 649 CVDL 652
Cdd:cd06127  154 TAEL 157
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 502-652 3.82e-06

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 47.48  E-value: 3.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 502 RVYALDCEMvyTIAGPALARLT---MVDMQRNRVLDVF---VKPPTDVLDPNTEFSGLTMEQINSAPdTLKTCHQKLFKY 575
Cdd:COG0847    1 RFVVLDTET--TGLDPAKDRIIeigAVKVDDGRIVETFhtlVNPERPIPPEATAIHGITDEDVADAP-PFAEVLPELLEF 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678 576 VnADTILIGHSLESDLKAMR---------VVHKNVIDTAILFRSTRDTKVALKvLSAKLLHKNIqgDNEDAigHDSMEDA 646
Cdd:COG0847   78 L-GGAVLVAHNAAFDLGFLNaelrraglpLPPFPVLDTLRLARRLLPGLPSYS-LDALCERLGI--PFDER--HRALADA 151


                 ....*.
gi 115532678 647 LTCVDL 652
Cdd:COG0847  152 EATAEL 157
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 505-652 2.33e-05

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 45.03  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  505 ALDCEMVYTIAGP----ALARLTmVDMQRNRVLDVFVKPPTDVLDPN-----TEFSGLTMEQINSAPdTLKTCHQKLFKY 575
Cdd:pfam00929   2 VIDLETTGLDPEKdeiiEIAAVV-IDGGENEIGETFHTYVKPTRLPKltdecTKFTGITQAMLDNKP-SFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  576 VNADTILIGHSLESDLK----AMRVVHKN-------VIDTAILFRSTRdTKVALKVLsAKLLHKniQGDNEDAIGHDSME 644
Cdd:pfam00929  80 LRKGNLLVAHNASFDVGflryDDKRFLKKpmpklnpVIDTLILDKATY-KELPGRSL-DALAEK--LGLEHIGRAHRALD 155


                  ....*...
gi 115532678  645 DALTCVDL 652
Cdd:pfam00929 156 DARATAKL 163
EloA-BP1 pfam15870
ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically ...
 243-389 3.25e-05

ElonginA binding-protein 1; This domain family is found in eukaryotes, and is typically between 144 and 167 amino acids in length.


Pssm-ID: 464914  Cd Length: 163  Bit Score: 44.67  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  243 PKILDFSVGRTFTAIRQTAIKLVFDTFLE-RDSPNAARE-AQEFELSIAKQYTDGQKYR---INIGHKvaaLRKE----- 312
Cdd:pfam15870   2 PVIPTEFGSKVPTNIRQRYLNLFIDECLKiCTSEQEAFErALEEEKAVYDRCSSKNIYLnvaVNTLKK---LRKEvpsqs 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 115532678  313 ---NTSGILEVNKNAVSHDKILAG--GPKDNCTVARGRKTHVDhrQLSIEKLHPLLLQFKLTTSELETNAYPMRR-DGST 386
Cdd:pfam15870  79 savTKSSAISSNNKVVSHEAVLGGklAAKTSFSINRNSKSIEE--DLKGATLYRMLKEYLLTEEQLKENGYPRPHpDKPG 156


                  ...
gi 115532678  387 KAV 389
Cdd:pfam15870 157 RAV 159
 
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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