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Conserved domains on  [gi|1370514798|ref|XP_024303380|]
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RNA exonuclease 4 isoform X1 [Homo sapiens]

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 ...
 107-257 7.30e-101

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: 291.34  E-value: 7.30e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRIL 186
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370514798 187 VGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLY 257
Cdd:cd06144    81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 107-257 7.30e-101

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: 291.34  E-value: 7.30e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRIL 186
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370514798 187 VGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLY 257
Cdd:cd06144    81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 107-265 1.38e-43

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 146.29  E-value: 1.38e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798  107 LALDCEMVGVGPKGEEsmAARVSIV---NQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKG 183
Cdd:smart00479   3 VVIDCETTGLDPGKDE--IIEIAAVdvdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798  184 RILV-GHALHNDLKVLFLDHPKKK--------IRDTQKYKPFKSQVKsGRPSLRLLSEKiLGLQVQQAEHCSIQDAQAAM 254
Cdd:smart00479  81 RILVaGNSAHFDLRFLKLEHPRLGikqppklpVIDTLKLARATNPGL-PKYSLKKLAKR-LLLEVIQRAHRALDDARATA 158

                          170
                   ....*....|.
gi 1370514798  255 RLYVMVKKEWE 265
Cdd:smart00479 159 KLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 107-257 3.18e-23

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: 93.18  E-value: 3.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEELEVVQKEVAEML 181
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 182 KG---------RILVGHALHNDLKVLFLDHPKkkIRDTQKYKPFKSQVKSGRPSLRL--LSEKiLGLQVQQAEHCSIQDA 250
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLKKPMPK--LNPVIDTLILDKATYKELPGRSLdaLAEK-LGLEHIGRAHRALDDA 157


                  ....*..
gi 1370514798 251 QAAMRLY 257
Cdd:pfam00929 158 RATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 105-257 5.57e-14

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 68.28  E-value: 5.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 105 RALALDCEMVGVGPKGEE--SMAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLK 182
Cdd:COG0847     1 RFVVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 183 GRILVGHALHNDLKVL-------FLDHPKKKIRDTQKykpFKSQVKSGRPSLRL--LSEKiLGLQVQQAeHCSIQDAQAA 253
Cdd:COG0847    80 GAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLR---LARRLLPGLPSYSLdaLCER-LGIPFDER-HRALADAEAT 154


                  ....
gi 1370514798 254 MRLY 257
Cdd:COG0847   155 AELF 158
PRK09145 PRK09145
3'-5' exonuclease;
108-262 1.03e-03

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 39.50  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 108 ALDCEMVGVGPKGEE--SMAArVSIVNqyGKCVYDK----YVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEML 181
Cdd:PRK09145   33 ALDCETTGLDPRRAEivSIAA-VKIRG--NRILTSErlelLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 182 KGRILVGHALHNDLKVL------FLDH--PKKKIRDTQKYKPFK-SQVKSGRPSLRLLS-EKILGLQVQQAeHCSIQDAQ 251
Cdd:PRK09145  110 GNRPLVGYYLEFDVAMLnryvrpLLGIplPNPLIEVSALYYDKKeRHLPDAYIDLRFDAiLKHLDLPVLGR-HDALNDAI 188

                         170
                  ....*....|.
gi 1370514798 252 AAMRLYVMVKK 262
Cdd:PRK09145  189 MAALIFLRLRK 199
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 142-259 2.51e-03

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 38.20  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 142 YVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRILVGHA-------LHNDLKVLFLDHPKK----KIRDT 210
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNasfdvgfLNYEFSKLYKVEPKTndviDTTDT 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1370514798 211 QKYkpFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVM 259
Cdd:TIGR00573 126 LQY--ARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLV 172
 
Name Accession Description Interval E-value
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 107-257 7.30e-101

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: 291.34  E-value: 7.30e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRIL 186
Cdd:cd06144     1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1370514798 187 VGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLY 257
Cdd:cd06144    81 VGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 107-257 1.25e-55

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: 176.86  E-value: 1.25e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRIL 186
Cdd:cd06149     1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1370514798 187 VGHALHNDLKVLFLDHPKKKIRDTQKYKPFKSQVK---SGRPSLRLLSEKIL--GLQVQQAEHCSIQDAQAAMRLY 257
Cdd:cd06149    81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGfpeNCRVSLKVLAKRLLhrDIQVGRQGHSSVEDARATMELY 156
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 107-256 6.79e-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: 154.18  E-value: 6.79e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGpKGEEsmAARVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQ-GEELEVVQKEVAEML-KGR 184
Cdd:cd06145     1 FALDCEMCYTT-DGLE--LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENvTTTLEDVQKKLLSLIsPDT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 185 ILVGHALHNDLKVLFLDHPkkKIRDT------QKYKPFKsqvksgrPSLRLLSEKILGLQVQQ--AEHCSIQDAQAAMRL 256
Cdd:cd06145    78 ILVGHSLENDLKALKLIHP--RVIDTailfphPRGPPYK-------PSLKNLAKKYLGRDIQQgeGGHDSVEDARAALEL 148
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 107-265 1.38e-43

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 146.29  E-value: 1.38e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798  107 LALDCEMVGVGPKGEEsmAARVSIV---NQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKG 183
Cdd:smart00479   3 VVIDCETTGLDPGKDE--IIEIAAVdvdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798  184 RILV-GHALHNDLKVLFLDHPKKK--------IRDTQKYKPFKSQVKsGRPSLRLLSEKiLGLQVQQAEHCSIQDAQAAM 254
Cdd:smart00479  81 RILVaGNSAHFDLRFLKLEHPRLGikqppklpVIDTLKLARATNPGL-PKYSLKKLAKR-LLLEVIQRAHRALDDARATA 158

                          170
                   ....*....|.
gi 1370514798  255 RLYVMVKKEWE 265
Cdd:smart00479 159 KLFKKLLERLE 169
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 108-257 5.34e-28

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: 105.44  E-value: 5.34e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 108 ALDCEMVGVGPKGEEsmAARVSIVNQY-GKCVYDKYVKPTEPVTDYRTAVSGIRPENL----KQGEEL---EVVQKEVAE 179
Cdd:cd06137     2 ALDCEMVGLADGDSE--VVRISAVDVLtGEVLIDSLVRPSVRVTDWRTRFSGVTPADLeeaaKAGKTIfgwEAARAALWK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 180 MLKGR-ILVGHALHNDLKVLFLDHPkkKIRDTqkYKPFKSQVK----SGRPSLRLLSEKILGLQVQQAE--HCSIQDAQA 252
Cdd:cd06137    80 FIDPDtILVGHSLQNDLDALRMIHT--RVVDT--AILTREAVKgplaKRQWSLRTLCRDFLGLKIQGGGegHDSLEDALA 155


                  ....*
gi 1370514798 253 AMRLY 257
Cdd:cd06137   156 AREVV 160
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 107-257 1.60e-25

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: 99.23  E-value: 1.60e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPK-------GEES------MA-ARVSIV----NQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENL---- 164
Cdd:cd06143     1 VAIDAEFVKLKPEeteirsdGTKStirpsqMSlARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLdpkt 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 165 --KQGEELEVVQKEVAEML-KGRILVGHALHNDLKVLFLDHPKKKIRDTQK--YKPfksqvKSGRPSLRLLSEKILGLQV 239
Cdd:cd06143    81 ssKNLTTLKSAYLKLRLLVdLGCIFVGHGLAKDFRVINIQVPKEQVIDTVElfHLP-----GQRKLSLRFLAWYLLGEKI 155

                         170
                  ....*....|....*...
gi 1370514798 240 QQAEHCSIQDAQAAMRLY 257
Cdd:cd06143   156 QSETHDSIEDARTALKLY 173
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 107-257 3.18e-23

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: 93.18  E-value: 3.18e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEESMA-ARVSIVN--QYGKCVYDKYVKPTEP--VTDYRTAVSGIRPENLKQGEELEVVQKEVAEML 181
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEiAAVVIDGgeNEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 182 KG---------RILVGHALHNDLKVLFLDHPKkkIRDTQKYKPFKSQVKSGRPSLRL--LSEKiLGLQVQQAEHCSIQDA 250
Cdd:pfam00929  81 RKgnllvahnaSFDVGFLRYDDKRFLKKPMPK--LNPVIDTLILDKATYKELPGRSLdaLAEK-LGLEHIGRAHRALDDA 157


                  ....*..
gi 1370514798 251 QAAMRLY 257
Cdd:pfam00929 158 RATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 107-257 3.72e-17

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: 76.57  E-value: 3.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 107 LALDCEMVGVGPKGEE--SMAArVSIVNQYGKCV-YDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKG 183
Cdd:cd06127     1 VVFDTETTGLDPKKDRiiEIGA-VKVDGGIEIVErFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 184 RILVGHALHNDLKVL-------FLDHPKKKIRDTQK-YKPFKSQVKSGRpsLRLLSEKILGLQVQQAeHCSIQDAQAAMR 255
Cdd:cd06127    80 RVLVAHNASFDLRFLnrelrrlGGPPLPNPWIDTLRlARRLLPGLRSHR--LGLLLAERYGIPLEGA-HRALADALATAE 156


                  ..
gi 1370514798 256 LY 257
Cdd:cd06127   157 LL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 105-257 5.57e-14

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 68.28  E-value: 5.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 105 RALALDCEMVGVGPKGEE--SMAArVSIVNQYGKCVYDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLK 182
Cdd:COG0847     1 RFVVLDTETTGLDPAKDRiiEIGA-VKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 183 GRILVGHALHNDLKVL-------FLDHPKKKIRDTQKykpFKSQVKSGRPSLRL--LSEKiLGLQVQQAeHCSIQDAQAA 253
Cdd:COG0847    80 GAVLVAHNAAFDLGFLnaelrraGLPLPPFPVLDTLR---LARRLLPGLPSYSLdaLCER-LGIPFDER-HRALADAEAT 154


                  ....
gi 1370514798 254 MRLY 257
Cdd:COG0847   155 AELF 158
PRK09145 PRK09145
3'-5' exonuclease;
108-262 1.03e-03

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 39.50  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 108 ALDCEMVGVGPKGEE--SMAArVSIVNqyGKCVYDK----YVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEML 181
Cdd:PRK09145   33 ALDCETTGLDPRRAEivSIAA-VKIRG--NRILTSErlelLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFI 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 182 KGRILVGHALHNDLKVL------FLDH--PKKKIRDTQKYKPFK-SQVKSGRPSLRLLS-EKILGLQVQQAeHCSIQDAQ 251
Cdd:PRK09145  110 GNRPLVGYYLEFDVAMLnryvrpLLGIplPNPLIEVSALYYDKKeRHLPDAYIDLRFDAiLKHLDLPVLGR-HDALNDAI 188

                         170
                  ....*....|.
gi 1370514798 252 AAMRLYVMVKK 262
Cdd:PRK09145  189 MAALIFLRLRK 199
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 139-256 1.37e-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: 38.74  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 139 YDKYVKPTE--PVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGR------------ILVGHALHNDLKVLFLDHPK 204
Cdd:cd06133    42 FSSYVKPVInpKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNgkyafvtwgdwdLKDLLQNQCKYKIINLPPFF 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1370514798 205 KKIRDTQKYkpFKSQVKSGRP-SLR-LLseKILGLQVQQAEHCSIQDAQAAMRL 256
Cdd:cd06133   122 RQWIDLKKE--FAKFYGLKKRtGLSkAL--EYLGLEFEGRHHRGLDDARNIARI 171
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 142-259 2.51e-03

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 38.20  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 142 YVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRILVGHA-------LHNDLKVLFLDHPKK----KIRDT 210
Cdd:TIGR00573  46 YIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNasfdvgfLNYEFSKLYKVEPKTndviDTTDT 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1370514798 211 QKYkpFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVM 259
Cdd:TIGR00573 126 LQY--ARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLV 172
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 110-202 5.43e-03

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 38.39  E-value: 5.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370514798 110 DCEMVGVGPKGEESMAARVSIVNQYGKCV--YDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRILV 187
Cdd:PRK08074    9 DLETTGNSPKKGDKIIQIAAVVVEDGEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFV 88

                          90
                  ....*....|....*
gi 1370514798 188 GHALHNDLKvlFLDH 202
Cdd:PRK08074   89 AHNVHFDLN--FLNE 101
polC PRK00448
DNA polymerase III PolC; Validated
 139-189 7.20e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 37.90  E-value: 7.20e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1370514798  139 YDKYVKPTEPVTDYRTAVSGIRPENLKQGEELEVVQKEVAEMLKGRILVGH 189
Cdd:PRK00448   455 FEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAH 505
 
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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