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Conserved domains on  [gi|320545860|ref|NP_001189105|]
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uncharacterized protein Dmel_CG6833, isoform B [Drosophila melanogaster]

Protein Classification

RNA exonuclease 4( domain architecture ID 10150217)

RNA exonuclease 4 is a DEDDh-type DnaQ-like 3'-5' exonuclease that functions in the processing and maturation of many RNA species

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676|GO:0006364|GO:0006281
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 118-270 1.43e-92

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: 270.54  E-value: 1.43e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVGVGHNTRDDMLARVSIVNRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRIL 197
Cdd:cd06144    1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320545860 198 VGHGLRNDLAVLGIRHPFHDIRDTSHYKPLCKLiSNTHTPSLKRLTKAVLGQEIQTGEHNSVEDARAAMGIYN 270
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKT-AKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 118-270 1.43e-92

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: 270.54  E-value: 1.43e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVGVGHNTRDDMLARVSIVNRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRIL 197
Cdd:cd06144    1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320545860 198 VGHGLRNDLAVLGIRHPFHDIRDTSHYKPLCKLiSNTHTPSLKRLTKAVLGQEIQTGEHNSVEDARAAMGIYN 270
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKT-AKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 116-277 3.83e-40

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 137.43  E-value: 3.83e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860   116 RILAMDCEMVGVGHNTrdDMLARVSIV---NRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLI 192
Cdd:smart00479   1 TLVVIDCETTGLDPGK--DEIIEIAAVdvdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860   193 HGRILV-GHGLRNDLAVLG--------IRHPFHDIRDTSHYKPlcKLISNTHTPSLKRLTKAVLGQEIQTgEHNSVEDAR 263
Cdd:smart00479  79 RGRILVaGNSAHFDLRFLKlehprlgiKQPPKLPVIDTLKLAR--ATNPGLPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155

                          170
                   ....*....|....
gi 320545860   264 AAMGIYNRVAVDWE 277
Cdd:smart00479 156 ATAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 118-269 3.03e-17

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: 77.01  E-value: 3.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860  118 LAMDCEMVGVgHNTRDDM--LARVSIVNRMGHVL--LDKYVKP--RKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKL 191
Cdd:pfam00929   1 VVIDLETTGL-DPEKDEIieIAAVVIDGGENEIGetFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860  192 I-HGRILVGHG-------LRNDLAVLGIRH--PFHDIRDTSHYkpLCKLISNTHTPSLKRLTKAVLGQEIQTgEHNSVED 261
Cdd:pfam00929  80 LrKGNLLVAHNasfdvgfLRYDDKRFLKKPmpKLNPVIDTLIL--DKATYKELPGRSLDALAEKLGLEHIGR-AHRALDD 156


                  ....*...
gi 320545860  262 ARAAMGIY 269
Cdd:pfam00929 157 ARATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 116-269 7.71e-15

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 70.59  E-value: 7.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 116 RILAMDCEMVGVGHnTRDDMLArVSIVNRMGHVLLDK---YVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLI 192
Cdd:COG0847    1 RFVVLDTETTGLDP-AKDRIIE-IGAVKVDDGRIVETfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 193 HGRILVGHGLRNDLAVL-------GIRHPFHDIRDT---SHykplcKLISNTHTPSLKRLTKAvLGQEIqTGEHNSVEDA 262
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTlrlAR-----RLLPGLPSYSLDALCER-LGIPF-DERHRALADA 151


                 ....*..
gi 320545860 263 RAAMGIY 269
Cdd:COG0847  152 EATAELF 158
PRK09145 PRK09145
3'-5' exonuclease;
119-209 1.68e-05

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 44.89  E-value: 1.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 119 AMDCEMVGVGHNtRDDMLARVSIVNRMGHVL----LDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHG 194
Cdd:PRK09145  33 ALDCETTGLDPR-RAEIVSIAAVKIRGNRILtserLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGN 111

                         90
                 ....*....|....*
gi 320545860 195 RILVGHGLRNDLAVL 209
Cdd:PRK09145 112 RPLVGYYLEFDVAML 126
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 118-270 1.43e-92

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: 270.54  E-value: 1.43e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVGVGHNTRDDMLARVSIVNRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRIL 197
Cdd:cd06144    1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320545860 198 VGHGLRNDLAVLGIRHPFHDIRDTSHYKPLCKLiSNTHTPSLKRLTKAVLGQEIQTGEHNSVEDARAAMGIYN 270
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKT-AKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 118-269 1.61e-52

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: 168.77  E-value: 1.61e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVGVGHNTRDDMLARVSIVNRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRIL 197
Cdd:cd06149    1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 320545860 198 VGHGLRNDLAVLGIRHPFHDIRDTSHYKPLCKL--ISNTHTPSLKRLTKAVLGQEIQTGE--HNSVEDARAAMGIY 269
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKagFPENCRVSLKVLAKRLLHRDIQVGRqgHSSVEDARATMELY 156
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 118-266 1.61e-47

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: 155.72  E-value: 1.61e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVgvgHNTRDDMLARVSIVNRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIAN-GEDFAAVQNEVMKLI-HGR 195
Cdd:cd06145    1 FALDCEMC---YTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENvTTTLEDVQKKLLSLIsPDT 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 320545860 196 ILVGHGLRNDLAVLGIRHPFhdIRDTSHYKPLCKliSNTHTPSLKRLTKAVLGQEIQT--GEHNSVEDARAAM 266
Cdd:cd06145   78 ILVGHSLENDLKALKLIHPR--VIDTAILFPHPR--GPPYKPSLKNLAKKYLGRDIQQgeGGHDSVEDARAAL 146
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 116-277 3.83e-40

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 137.43  E-value: 3.83e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860   116 RILAMDCEMVGVGHNTrdDMLARVSIV---NRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLI 192
Cdd:smart00479   1 TLVVIDCETTGLDPGK--DEIIEIAAVdvdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860   193 HGRILV-GHGLRNDLAVLG--------IRHPFHDIRDTSHYKPlcKLISNTHTPSLKRLTKAVLGQEIQTgEHNSVEDAR 263
Cdd:smart00479  79 RGRILVaGNSAHFDLRFLKlehprlgiKQPPKLPVIDTLKLAR--ATNPGLPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155

                          170
                   ....*....|....
gi 320545860   264 AAMGIYNRVAVDWE 277
Cdd:smart00479 156 ATAKLFKKLLERLE 169
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 119-269 2.26e-31

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: 114.30  E-value: 2.26e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 119 AMDCEMVGVGHNtrDDMLARVSIVNRM-GHVLLDKYVKPRKEVTDYRTSVSGIRPQDIANGED-------FAAVQNEVMK 190
Cdd:cd06137    2 ALDCEMVGLADG--DSEVVRISAVDVLtGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAKagktifgWEAARAALWK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 191 LIHGR-ILVGHGLRNDLAVLGIRHPfhDIRDTS----HY--KPLCKlisntHTPSLKRLTKAVLGQEIQTGE--HNSVED 261
Cdd:cd06137   80 FIDPDtILVGHSLQNDLDALRMIHT--RVVDTAiltrEAvkGPLAK-----RQWSLRTLCRDFLGLKIQGGGegHDSLED 152


                 ....*...
gi 320545860 262 ARAAMGIY 269
Cdd:cd06137  153 ALAAREVV 160
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 136-269 4.39e-24

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: 95.76  E-value: 4.39e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 136 LARVSIV----NRMGHVLLDKYVKPRKEVTDYRTSVSGIRPQDI--ANGEDFAAVQNEVMKLIH-----GRILVGHGLRN 204
Cdd:cd06143   33 LARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLdpKTSSKNLTTLKSAYLKLRllvdlGCIFVGHGLAK 112

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 320545860 205 DLAVLGIRHPFHDIRDTSH--YKPLCKLISnthtpsLKRLTKAVLGQEIQTGEHNSVEDARAAMGIY 269
Cdd:cd06143  113 DFRVINIQVPKEQVIDTVElfHLPGQRKLS------LRFLAWYLLGEKIQSETHDSIEDARTALKLY 173
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 118-269 3.03e-17

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: 77.01  E-value: 3.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860  118 LAMDCEMVGVgHNTRDDM--LARVSIVNRMGHVL--LDKYVKP--RKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKL 191
Cdd:pfam00929   1 VVIDLETTGL-DPEKDEIieIAAVVIDGGENEIGetFHTYVKPtrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860  192 I-HGRILVGHG-------LRNDLAVLGIRH--PFHDIRDTSHYkpLCKLISNTHTPSLKRLTKAVLGQEIQTgEHNSVED 261
Cdd:pfam00929  80 LrKGNLLVAHNasfdvgfLRYDDKRFLKKPmpKLNPVIDTLIL--DKATYKELPGRSLDALAEKLGLEHIGR-AHRALDD 156


                  ....*...
gi 320545860  262 ARAAMGIY 269
Cdd:pfam00929 157 ARATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 116-269 7.71e-15

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 70.59  E-value: 7.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 116 RILAMDCEMVGVGHnTRDDMLArVSIVNRMGHVLLDK---YVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLI 192
Cdd:COG0847    1 RFVVLDTETTGLDP-AKDRIIE-IGAVKVDDGRIVETfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 193 HGRILVGHGLRNDLAVL-------GIRHPFHDIRDT---SHykplcKLISNTHTPSLKRLTKAvLGQEIqTGEHNSVEDA 262
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTlrlAR-----RLLPGLPSYSLDALCER-LGIPF-DERHRALADA 151


                 ....*..
gi 320545860 263 RAAMGIY 269
Cdd:COG0847  152 EATAELF 158
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 118-270 1.08e-12

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: 64.63  E-value: 1.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 118 LAMDCEMVGVgHNTRDDM--LARVSIVNRMGHV-LLDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHG 194
Cdd:cd06127    1 VVFDTETTGL-DPKKDRIieIGAVKVDGGIEIVeRFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 195 RILVGHGLRNDLAVLgiRHPFHDIRDTSHYKP-LC------KLISNTHTPSLKRLTKAVLGQEiQTGEHNSVEDARAAMG 267
Cdd:cd06127   80 RVLVAHNASFDLRFL--NRELRRLGGPPLPNPwIDtlrlarRLLPGLRSHRLGLLLAERYGIP-LEGAHRALADALATAE 156


                 ...
gi 320545860 268 IYN 270
Cdd:cd06127  157 LLL 159
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 153-269 3.38e-08

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a 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: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 51.74  E-value: 3.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 153 YVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRILVGHGLRNDLAVLGIRHPFHDIrDTSHYKPLC---- 228
Cdd:cd06130   36 LIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGL-PPPPYQYLCtvrl 114

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 320545860 229 -----KLISNTHTPSLKRltkaVLGQEIQtgEHNSVEDARAAMGIY 269
Cdd:cd06130  115 arrvwPLLPNHKLNTVAE----HLGIELN--HHDALEDARACAEIL 154
PRK09145 PRK09145
3'-5' exonuclease;
119-209 1.68e-05

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 44.89  E-value: 1.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 119 AMDCEMVGVGHNtRDDMLARVSIVNRMGHVL----LDKYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHG 194
Cdd:PRK09145  33 ALDCETTGLDPR-RAEIVSIAAVKIRGNRILtserLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIGN 111

                         90
                 ....*....|....*
gi 320545860 195 RILVGHGLRNDLAVL 209
Cdd:PRK09145 112 RPLVGYYLEFDVAML 126
PRK07740 PRK07740
hypothetical protein; Provisional
 121-287 2.22e-05

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 44.66  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 121 DCEMVGVGHNTRDDMLARVSIVNRMGHVLLDKY---VKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRIL 197
Cdd:PRK07740  65 DLETTGFSPQQGDEILSIGAVKTKGGEVETDTFyslVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIGAGVL 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 198 VGHGLRNDLAVLG------IRHPF-HDIRDTShykPLCKLISN-THTPSLKRLTkAVLGQEIqTGEHNSVEDARAAmgiy 269
Cdd:PRK07740 145 VAHHAGHDKAFLRhalwrtYRQPFtHRLIDTM---FLTKLLAHeRDFPTLDDAL-AYYGIPI-PRRHHALGDALMT---- 215

                        170
                 ....*....|....*...
gi 320545860 270 nrvAVDWEKYLEKKRHQQ 287
Cdd:PRK07740 216 ---AKLWAILLVEAQQRG 230
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 152-209 3.22e-04

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 42.25  E-value: 3.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 320545860 152 KYVKPRKEVTDYRTSVSGIRPQDIANGEDFAAVQNEVMKLIHGRILVGHGLRNDLAVL 209
Cdd:PRK08074  42 SFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFVAHNVHFDLNFL 99
WRN_exo cd06141
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ...
 196-290 4.85e-04

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: 39.87  E-value: 4.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 196 ILVGHGLRNDLAVLGIRHPFHD--IRDTSHykpLCKLISNTHTP-SLKRLTKAVLGQEIQTgehnsveDARAAMGiynrv 272
Cdd:cd06141   75 LKVGVGIKGDARKLARDFGIEVrgVVDLSH---LAKRVGPRRKLvSLARLVEEVLGLPLSK-------PKKVRCS----- 139

                         90
                 ....*....|....*....
gi 320545860 273 avDWEKY-LekkRHQQQHY 290
Cdd:cd06141  140 --NWEARpL---SKEQILY 153
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 117-263 4.85e-03

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These 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. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 37.20  E-value: 4.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 117 ILAMDCEMVGVGHNTRDDMLAR-----VSIVNRMGHVLLDK---YVKPR--KEVTDYRTSVSGIRPQDIANGEDFAAVQN 186
Cdd:cd06133    1 YLVIDFEATCWEGNSKPDYPNEiieigAVLVDVKTKEIIDTfssYVKPVinPKLSDFCTELTGITQEDVDNAPSFPEVLK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320545860 187 EVMKLIHGR---ILVGHGlRNDLAVL--------GIRHP-----FHDIRDTshYKplcKLISNTHTPSLKRLtKAVLGQE 250
Cdd:cd06133   81 EFLEWLGKNgkyAFVTWG-DWDLKDLlqnqckykIINLPpffrqWIDLKKE--FA---KFYGLKKRTGLSKA-LEYLGLE 153

                        170
                 ....*....|...
gi 320545860 251 IQTGEHNSVEDAR 263
Cdd:cd06133  154 FEGRHHRGLDDAR 166
 
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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