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Conserved domains on  [gi|1063707175|ref|NP_001323898|]
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Exonuclease family protein [Arabidopsis thaliana]

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 ...
 134-291 1.19e-76

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: 232.02  E-value: 1.19e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADGTIDQCASVCLVDDDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLCGgqnd 213
Cdd:cd06144     2 ALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKG---- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063707175 214 gagrLLLVGHDLRHDMSCLKLEYPSHLLRDTAKYVPLMKTNL-VSQSLKYLTKSYLGYKIQCGKHEVYEDCVSAMRLYK 291
Cdd:cd06144    78 ----RILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKgKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 134-291 1.19e-76

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: 232.02  E-value: 1.19e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADGTIDQCASVCLVDDDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLCGgqnd 213
Cdd:cd06144     2 ALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKG---- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063707175 214 gagrLLLVGHDLRHDMSCLKLEYPSHLLRDTAKYVPLMKTNL-VSQSLKYLTKSYLGYKIQCGKHEVYEDCVSAMRLYK 291
Cdd:cd06144    78 ----RILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKgKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 134-298 4.01e-41

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 141.67  E-value: 4.01e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175  134 ALDCEMVGGGADGtiDQCASVCLVD---DDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcgg 210
Cdd:smart00479   4 VIDCETTGLDPGK--DEIIEIAAVDvdgGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL--- 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175  211 qndgAGRLLLVGHDLRHDMSCLKLEYP--------SHLLRDTAKYVPLMKTNLVSQSLKYLTKSYLGYKIQCGkHEVYED 282
Cdd:smart00479  79 ----RGRILVAGNSAHFDLRFLKLEHPrlgikqppKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRA-HRALDD 153

                          170
                   ....*....|....*.
gi 1063707175  283 CVSAMRLYKRMRDQEH 298
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 134-290 1.30e-12

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: 65.07  E-value: 1.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADG-TIDQCASVcLVDDDENVI---FSTHVQPLLP--VTDYRHEITGLTKEDLKDGMPLEHVRERVFSFL 207
Cdd:pfam00929   2 VIDLETTGLDPEKdEIIEIAAV-VIDGGENEIgetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 208 CGGQndgagrlLLVGH-------DLRHDMS-CLKLEYPshLLRDTAKYVPLMK---TNLVSQSLKYLTKSYLGYKIQcGK 276
Cdd:pfam00929  81 RKGN-------LLVAHnasfdvgFLRYDDKrFLKKPMP--KLNPVIDTLILDKatyKELPGRSLDALAEKLGLEHIG-RA 150

                         170
                  ....*....|....
gi 1063707175 277 HEVYEDCVSAMRLY 290
Cdd:pfam00929 151 HRALDDARATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 134-295 1.18e-10

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 59.42  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMvgGGADGTIDQCASVCLVDDDENVI---FSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcgg 210
Cdd:COG0847     4 VLDTET--TGLDPAKDRIIEIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL--- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 211 qnDGAgrlLLVGHDLRHDMSCLK-------LEYPSHLLRDTAKYVPLMKTNLVSQSLKYLTKsYLGYKIQcGKHEVYEDC 283
Cdd:COG0847    79 --GGA---VLVAHNAAFDLGFLNaelrragLPLPPFPVLDTLRLARRLLPGLPSYSLDALCE-RLGIPFD-ERHRALADA 151

                         170
                  ....*....|..
gi 1063707175 284 VSAMRLYKRMRD 295
Cdd:COG0847   152 EATAELFLALLR 163
PRK06807 PRK06807
3'-5' exonuclease;
165-327 1.26e-05

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 46.35  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 165 FSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcggqndgaGRLLLVGHDLRHDMSCLK-------LEYP 237
Cdd:PRK06807   44 FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL--------HTNVIVAHNASFDMRFLKsnvnmlgLPEP 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 238 SHLLRDTAKYVPLMKTNLVSQSLKYLtKSYLGykIQCGKHEVYEDCVSAMRLYKRmrdqehvCSGKAEgnglNSRKQSDL 317
Cdd:PRK06807  116 KNKVIDTVFLAKKYMKHAPNHKLETL-KRMLG--IRLSSHNAFDDCITCAAVYQK-------CASIEE----EAKRKSNK 181

                         170
                  ....*....|
gi 1063707175 318 EKMNAEELYQ 327
Cdd:PRK06807  182 EVLDETAVYE 191
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 134-291 1.19e-76

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: 232.02  E-value: 1.19e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADGTIDQCASVCLVDDDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLCGgqnd 213
Cdd:cd06144     2 ALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKG---- 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063707175 214 gagrLLLVGHDLRHDMSCLKLEYPSHLLRDTAKYVPLMKTNL-VSQSLKYLTKSYLGYKIQCGKHEVYEDCVSAMRLYK 291
Cdd:cd06144    78 ----RILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKgKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 134-298 4.01e-41

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 141.67  E-value: 4.01e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175  134 ALDCEMVGGGADGtiDQCASVCLVD---DDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcgg 210
Cdd:smart00479   4 VIDCETTGLDPGK--DEIIEIAAVDvdgGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL--- 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175  211 qndgAGRLLLVGHDLRHDMSCLKLEYP--------SHLLRDTAKYVPLMKTNLVSQSLKYLTKSYLGYKIQCGkHEVYED 282
Cdd:smart00479  79 ----RGRILVAGNSAHFDLRFLKLEHPrlgikqppKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRA-HRALDD 153

                          170
                   ....*....|....*.
gi 1063707175  283 CVSAMRLYKRMRDQEH 298
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 133-291 5.32e-28

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: 106.75  E-value: 5.32e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 133 MALDCEMVGGGADGTIDQCASVCLVDDDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLCGGqn 212
Cdd:cd06149     1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGK-- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 213 dgagrlLLVGHDLRHDMSCLKLEYPSHLLRDTAKYVPLMKTNLVSQ----SLKYLTKSYLGYKIQCGK--HEVYEDCVSA 286
Cdd:cd06149    79 ------VVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPEncrvSLKVLAKRLLHRDIQVGRqgHSSVEDARAT 152


                  ....*
gi 1063707175 287 MRLYK 291
Cdd:cd06149   153 MELYK 157
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 134-291 7.27e-28

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: 106.03  E-value: 7.27e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMV--GGGadgtiDQCASVCLVDDDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKD-GMPLEHVRERVFSFLcgg 210
Cdd:cd06145     2 ALDCEMCytTDG-----LELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENvTTTLEDVQKKLLSLI--- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 211 qNDGAgrlLLVGHDLRHDMSCLKLEYP-----SHLLRDTAKYVPlmktnlvSQSLKYLTKSYLGYKIQCGK--HEVYEDC 283
Cdd:cd06145    74 -SPDT---ILVGHSLENDLKALKLIHPrvidtAILFPHPRGPPY-------KPSLKNLAKKYLGRDIQQGEggHDSVEDA 142


                  ....*...
gi 1063707175 284 VSAMRLYK 291
Cdd:cd06145   143 RAALELVK 150
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 134-290 9.80e-18

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: 79.25  E-value: 9.80e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADGtiDQCASVCLVD-DDENVIFSTHVQPLLPVTDYRHEITGLTKEDLKD-------GMPLEHVRERVFS 205
Cdd:cd06137     2 ALDCEMVGLADGD--SEVVRISAVDvLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEaakagktIFGWEAARAALWK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 206 FLcggqndgAGRLLLVGHDLRHDMSCLKLEYP----SHLLRDTAKYVPLMKTNLvsqSLKYLTKSYLGYKIQCGK--HEV 279
Cdd:cd06137    80 FI-------DPDTILVGHSLQNDLDALRMIHTrvvdTAILTREAVKGPLAKRQW---SLRTLCRDFLGLKIQGGGegHDS 149

                         170
                  ....*....|.
gi 1063707175 280 YEDCVSAMRLY 290
Cdd:cd06137   150 LEDALAAREVV 160
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 134-290 1.30e-12

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: 65.07  E-value: 1.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMVGGGADG-TIDQCASVcLVDDDENVI---FSTHVQPLLP--VTDYRHEITGLTKEDLKDGMPLEHVRERVFSFL 207
Cdd:pfam00929   2 VIDLETTGLDPEKdEIIEIAAV-VIDGGENEIgetFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 208 CGGQndgagrlLLVGH-------DLRHDMS-CLKLEYPshLLRDTAKYVPLMK---TNLVSQSLKYLTKSYLGYKIQcGK 276
Cdd:pfam00929  81 RKGN-------LLVAHnasfdvgFLRYDDKrFLKKPMP--KLNPVIDTLILDKatyKELPGRSLDALAEKLGLEHIG-RA 150

                         170
                  ....*....|....
gi 1063707175 277 HEVYEDCVSAMRLY 290
Cdd:pfam00929 151 HRALDDARATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 134-295 1.18e-10

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 59.42  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 134 ALDCEMvgGGADGTIDQCASVCLVDDDENVI---FSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcgg 210
Cdd:COG0847     4 VLDTET--TGLDPAKDRIIEIGAVKVDDGRIvetFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL--- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 211 qnDGAgrlLLVGHDLRHDMSCLK-------LEYPSHLLRDTAKYVPLMKTNLVSQSLKYLTKsYLGYKIQcGKHEVYEDC 283
Cdd:COG0847    79 --GGA---VLVAHNAAFDLGFLNaelrragLPLPPFPVLDTLRLARRLLPGLPSYSLDALCE-RLGIPFD-ERHRALADA 151

                         170
                  ....*....|..
gi 1063707175 284 VSAMRLYKRMRD 295
Cdd:COG0847   152 EATAELFLALLR 163
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 174-291 2.32e-07

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: 49.92  E-value: 2.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 174 PVTDYRHEITGLTKEDL------KDGMPLEHVRERVfsflcggqndgagRLLL------VGHDLRHDMSCLKLEYPSHLL 241
Cdd:cd06143    60 PVVDYLTRFSGIKPGDLdpktssKNLTTLKSAYLKL-------------RLLVdlgcifVGHGLAKDFRVINIQVPKEQV 126

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063707175 242 RDTAKYVPLMKTNLVSqsLKYLTKSYLGYKIQCGKHEVYEDCVSAMRLYK 291
Cdd:cd06143   127 IDTVELFHLPGQRKLS--LRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174
PRK06807 PRK06807
3'-5' exonuclease;
165-327 1.26e-05

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 46.35  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 165 FSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLcggqndgaGRLLLVGHDLRHDMSCLK-------LEYP 237
Cdd:PRK06807   44 FVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL--------HTNVIVAHNASFDMRFLKsnvnmlgLPEP 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 238 SHLLRDTAKYVPLMKTNLVSQSLKYLtKSYLGykIQCGKHEVYEDCVSAMRLYKRmrdqehvCSGKAEgnglNSRKQSDL 317
Cdd:PRK06807  116 KNKVIDTVFLAKKYMKHAPNHKLETL-KRMLG--IRLSSHNAFDDCITCAAVYQK-------CASIEE----EAKRKSNK 181

                         170
                  ....*....|
gi 1063707175 318 EKMNAEELYQ 327
Cdd:PRK06807  182 EVLDETAVYE 191
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 153-213 2.04e-04

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: 41.44  E-value: 2.04e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063707175 153 SVCLVDDDENVI---FSTHVQPLL--PVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFLCGGQND 213
Cdd:cd06133    27 GAVLVDVKTKEIidtFSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKY 92
PRK07740 PRK07740
hypothetical protein; Provisional
 161-292 2.18e-04

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 41.96  E-value: 2.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 161 ENVIFSTHVQPLLPVTDYRHEITGLTKEDLKDGMPLEHVRERVFSFlcggqndgAGRLLLVGHDLRHDMSCL-------- 232
Cdd:PRK07740   93 ETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF--------IGAGVLVAHHAGHDKAFLrhalwrty 164

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063707175 233 KLEYpSHLLRDTAKYVPLMKTNLVSQSLKYLTKSYlGYKIQcGKHEVYEDCVSAMRLYKR 292
Cdd:PRK07740  165 RQPF-THRLIDTMFLTKLLAHERDFPTLDDALAYY-GIPIP-RRHHALGDALMTAKLWAI 221
 
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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