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Conserved domains on  [gi|15229667|ref|NP_190578|]
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Exonuclease family protein [Arabidopsis thaliana]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ_like_exo super family cl10012
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 76-205 2.81e-49

DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer.


The actual alignment was detected with superfamily member cd06145:

Pssm-ID: 447876  Cd Length: 150  Bit Score: 161.50  E-value: 2.81e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  76 LALDCEMVLCEDGTEgVVRVGAVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATLSLVDIQEKLRPFLSAGAIL 155
Cdd:cd06145   1 FALDCEMCYTTDGLE-LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229667 156 I-------------DHPIVIDTSLVFKYPNSRKlRRPSLNTLCMSVLGYEVQKAGVSHHCVHD 205
Cdd:cd06145  80 VghslendlkalklIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQQGEGGHDSVED 141
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 76-205 2.81e-49

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: 161.50  E-value: 2.81e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  76 LALDCEMVLCEDGTEgVVRVGAVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATLSLVDIQEKLRPFLSAGAIL 155
Cdd:cd06145   1 FALDCEMCYTTDGLE-LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229667 156 I-------------DHPIVIDTSLVFKYPNSRKlRRPSLNTLCMSVLGYEVQKAGVSHHCVHD 205
Cdd:cd06145  80 VghslendlkalklIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQQGEGGHDSVED 141
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 75-196 1.10e-16

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 76.18  E-value: 1.10e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667     75 MLALDCEMVLCEDGTEGVVRVGAVD---RNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATlSLVDIQEKLRPFLSA 151
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDvdgGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFLRG 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15229667    152 GAILIDH-----------------------PIVIDTSLVFKYPNSRkLRRPSLNTLCMSVLGYEVQKA 196
Cdd:smart00479  81 RILVAGNsahfdlrflklehprlgikqppkLPVIDTLKLARATNPG-LPKYSLKKLAKRLLLEVIQRA 147
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 91-185 9.52e-06

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 45.52  E-value: 9.52e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  91 GVVRVgavdRNLKVI--LDEFVKPHKPVVDYRTAITGVTAEDVQKAtlslVDIQEKLRPFLS--AGAILIDH-------- 158
Cdd:COG2176  31 GAVKV----ENGEIVdrFSTLVNPGRPIPPFITELTGITDEMVADA----PPFEEVLPEFLEflGDAVLVAHnasfdlgf 102

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15229667 159 -------------PIVIDTSLVFK--YPNsrkLRRPSLNTLC 185
Cdd:COG2176 103 lnaalkrlglpfdNPVLDTLELARrlLPE---LKSYKLDTLA 141
polC PRK00448
DNA polymerase III PolC; Validated
 96-268 8.27e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 44.44  E-value: 8.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667    96 GAVD-RNLKVI--LDEFVKPHKPVVDYRTAITGVTAEDVQKAtlslVDIQEKLRPFLS--AGAILIDH------------ 158
Cdd:PRK00448  442 GAVKiKNGEIIdkFEFFIKPGHPLSAFTTELTGITDDMVKDA----PSIEEVLPKFKEfcGDSILVAHnasfdvgfintn 517

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667   159 ----------PIVIDTsLV---FKYPNsrkLRRPSLNTLCmsvlgyevQKAGVS---HHCVHDaaaamklalavikkrvD 222
Cdd:PRK00448  518 yeklglekikNPVIDT-LElsrFLYPE---LKSHRLNTLA--------KKFGVElehHHRADY----------------D 569

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15229667   223 TTIT-------LTKEAEKSRLFLHRIPHHLSSEELKKdlalKFFPKNFTIDVK 268
Cdd:PRK00448  570 AEATayllikfLKDLKEKGITNLDELNKKLGSEDAYK----KARPKHATILVK 618
 
Name Accession Description Interval E-value
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 76-205 2.81e-49

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: 161.50  E-value: 2.81e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  76 LALDCEMVLCEDGTEgVVRVGAVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATLSLVDIQEKLRPFLSAGAIL 155
Cdd:cd06145   1 FALDCEMCYTTDGLE-LTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTTLEDVQKKLLSLISPDTIL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229667 156 I-------------DHPIVIDTSLVFKYPNSRKlRRPSLNTLCMSVLGYEVQKAGVSHHCVHD 205
Cdd:cd06145  80 VghslendlkalklIHPRVIDTAILFPHPRGPP-YKPSLKNLAKKYLGRDIQQGEGGHDSVED 141
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 76-205 9.76e-29

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: 107.99  E-value: 9.76e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  76 LALDCEMVLC-EDGTEGVV-RVGAVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATlSLVDIQEKLRPFLsAGA 153
Cdd:cd06144   1 VALDCEMVGVgPDGSESALaRVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAP-DFEEVQKKVAELL-KGR 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15229667 154 ILI-------------DHP--IVIDTSLVFKYPNSRKLRRPSLNTLCMSVLGYEVQKAgvSHHCVHD 205
Cdd:cd06144  79 ILVghalkndlkvlklDHPkkLIRDTSKYKPLRKTAKGKSPSLKKLAKQLLGLDIQEG--EHSSVED 143
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 77-205 7.89e-22

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: 90.03  E-value: 7.89e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  77 ALDCEMVLCEDGTEGVVRVGAVDRNL-KVILDEFVKPHKPVVDYRTAITGVTAEDVQKA-----TLS--LVDIQEKLRpF 148
Cdd:cd06137   2 ALDCEMVGLADGDSEVVRISAVDVLTgEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAakagkTIFgwEAARAALWK-F 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229667 149 LSAGAILI-------------DHPIVIDTSLVFKYPNSRKLRRP--SLNTLCMSVLGYEVQKAGVSHHCVHD 205
Cdd:cd06137  81 IDPDTILVghslqndldalrmIHTRVVDTAILTREAVKGPLAKRqwSLRTLCRDFLGLKIQGGGEGHDSLED 152
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 75-196 1.10e-16

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 76.18  E-value: 1.10e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667     75 MLALDCEMVLCEDGTEGVVRVGAVD---RNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATlSLVDIQEKLRPFLSA 151
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDvdgGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAP-TFEEVLEELLEFLRG 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15229667    152 GAILIDH-----------------------PIVIDTSLVFKYPNSRkLRRPSLNTLCMSVLGYEVQKA 196
Cdd:smart00479  81 RILVAGNsahfdlrflklehprlgikqppkLPVIDTLKLARATNPG-LPKYSLKKLAKRLLLEVIQRA 147
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 76-203 2.14e-09

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: 55.52  E-value: 2.14e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  76 LALDCEMVLCEDG--TEGVVRVGAVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKATLSLVDIQEKLRpfLSAGA 153
Cdd:cd06149   1 VAIDCEMVGTGPGgrESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILK--ILKGK 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15229667 154 ILIDHPIVIDTSlVFKYPNSRKLRR-----PSLNtlcmsvlgyevQKAGVSHHCV 203
Cdd:cd06149  79 VVVGHAIHNDFK-ALKYFHPKHMTRdtstiPLLN-----------RKAGFPENCR 121
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 81-194 3.07e-06

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: 46.84  E-value: 3.07e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  81 EMVLCEDGTE--------GVVRVGAV----DRNLKVILDEFVKPHKPVVDYRTAITGVTAEDV-----QKATLSLVDIQE 143
Cdd:cd06143  14 ETEIRSDGTKstirpsqmSLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLdpktsSKNLTTLKSAYL 93

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229667 144 KLRPFLSAGAILIDHPI---------------VIDTSLVFKYPNSRKLrrpSLNTLCMSVLGYEVQ 194
Cdd:cd06143  94 KLRLLVDLGCIFVGHGLakdfrviniqvpkeqVIDTVELFHLPGQRKL---SLRFLAWYLLGEKIQ 156
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 91-185 9.52e-06

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 45.52  E-value: 9.52e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  91 GVVRVgavdRNLKVI--LDEFVKPHKPVVDYRTAITGVTAEDVQKAtlslVDIQEKLRPFLS--AGAILIDH-------- 158
Cdd:COG2176  31 GAVKV----ENGEIVdrFSTLVNPGRPIPPFITELTGITDEMVADA----PPFEEVLPEFLEflGDAVLVAHnasfdlgf 102

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15229667 159 -------------PIVIDTSLVFK--YPNsrkLRRPSLNTLC 185
Cdd:COG2176 103 lnaalkrlglpfdNPVLDTLELARrlLPE---LKSYKLDTLA 141
polC PRK00448
DNA polymerase III PolC; Validated
 96-268 8.27e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 44.44  E-value: 8.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667    96 GAVD-RNLKVI--LDEFVKPHKPVVDYRTAITGVTAEDVQKAtlslVDIQEKLRPFLS--AGAILIDH------------ 158
Cdd:PRK00448  442 GAVKiKNGEIIdkFEFFIKPGHPLSAFTTELTGITDDMVKDA----PSIEEVLPKFKEfcGDSILVAHnasfdvgfintn 517

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667   159 ----------PIVIDTsLV---FKYPNsrkLRRPSLNTLCmsvlgyevQKAGVS---HHCVHDaaaamklalavikkrvD 222
Cdd:PRK00448  518 yeklglekikNPVIDT-LElsrFLYPE---LKSHRLNTLA--------KKFGVElehHHRADY----------------D 569

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 15229667   223 TTIT-------LTKEAEKSRLFLHRIPHHLSSEELKKdlalKFFPKNFTIDVK 268
Cdd:PRK00448  570 AEATayllikfLKDLKEKGITNLDELNKKLGSEDAYK----KARPKHATILVK 618
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 91-185 8.41e-05

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 42.47  E-value: 8.41e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  91 GVVRVgaVDRNLKVILDEFVKPHKPVVDYRTAITGVTAEDVQKAtLSLVDIQEKLRPFLsAGAILI------DHPI---- 160
Cdd:COG0847  23 GAVKV--DDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADA-PPFAEVLPELLEFL-GGAVLVahnaafDLGFlnae 98

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 15229667 161 ------------VIDTSLVFK--YPNsrkLRRPSLNTLC 185
Cdd:COG0847  99 lrraglplppfpVLDTLRLARrlLPG---LPSYSLDALC 134
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 76-134 1.61e-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: 1.61e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229667  76 LALDCEMvLCEDGTEG------VVRVGAV--DRNLKVILDEF---VKP--HKPVVDYRTAITGVTAEDVQKA 134
Cdd:cd06133   2 LVIDFEA-TCWEGNSKpdypneIIEIGAVlvDVKTKEIIDTFssyVKPviNPKLSDFCTELTGITQEDVDNA 72
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 91-201 7.32e-03

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: 36.34  E-value: 7.32e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229667  91 GVVRVgavdRNLKVIlDEF---VKPHKPVVDYRTAITGVTAEDVQKATlSLVDIQEKLRPFLsAGAILIDHPIVIDTSlV 167
Cdd:cd06130  20 GLVKV----RDGQIV-DTFytlIRPPTRFDPFNIAIHGITPEDVADAP-TFPEVWPEIKPFL-GGSLVVAHNASFDRS-V 91

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15229667 168 FK---------YPN---------SRK----LRRPSLNTLCmSVLGYEVQkagvsHH 201
Cdd:cd06130  92 LRaaleayglpPPPyqylctvrlARRvwplLPNHKLNTVA-EHLGIELN-----HH 141
 
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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