NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|530407250|ref|XP_005255023|]
View 

apoptosis-enhancing nuclease isoform X1 [Homo sapiens]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 111-267 1.31e-90

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 cd06149:

Pssm-ID: 447876  Cd Length: 157  Bit Score: 267.38  E-value: 1.31e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVV 190
Cdd:cd06149    1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530407250 191 VGHALHNDFQALKYVHPRSQTRDTTYVPNFLSEPGLHTRARVSLKDLALQLLHKKIQVGQHGHSSVEDATTAMELYR 267
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 111-267 1.31e-90

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: 267.38  E-value: 1.31e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVV 190
Cdd:cd06149    1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530407250 191 VGHALHNDFQALKYVHPRSQTRDTTYVPNFLSEPGLHTRARVSLKDLALQLLHKKIQVGQHGHSSVEDATTAMELYR 267
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 111-274 1.36e-38

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 134.35  E-value: 1.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250   111 VAIDCEMVGTGPRGrvSELARCSIVSYHGN---VLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKG 187
Cdd:smart00479   3 VVIDCETTGLDPGK--DEIIEIAAVDVDGGeiiEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250   188 KV-VVGHALHNDFQALKYVHPR--------SQTRDT-TYVPNFLSEPGlhtraRVSLKDLALQLLHKKIqvgQHGHSSVE 257
Cdd:smart00479  81 RIlVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTlKLARATNPGLP-----KYSLKKLAKRLLLEVI---QRAHRALD 152

                          170
                   ....*....|....*..
gi 530407250   258 DATTAMELYRLVEVQWE 274
Cdd:smart00479 153 DARATAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 111-266 1.13e-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: 78.93  E-value: 1.13e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250  111 VAIDCEMVGTGPRG-RVSELARCSIVSY--HGNVLYDKYIRPEMP--IADYRTRWSGITRQHMRKAVPFQVAQKEILKLL 185
Cdd:pfam00929   1 VVIDLETTGLDPEKdEIIEIAAVVIDGGenEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250  186 -KGKVVVGH--------ALHNDFQALKYVHP-RSQTRDttYVPNFLSEPGLhtRARVSLKDLALQLLHKKIqvgQHGHSS 255
Cdd:pfam00929  81 rKGNLLVAHnasfdvgfLRYDDKRFLKKPMPkLNPVID--TLILDKATYKE--LPGRSLDALAEKLGLEHI---GRAHRA 153

                         170
                  ....*....|.
gi 530407250  256 VEDATTAMELY 266
Cdd:pfam00929 154 LDDARATAKLF 164
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 111-267 3.95e-13

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 66.36  E-value: 3.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP-RGRVSELArcsIVSYHGNVLYDK---YIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLK 186
Cdd:COG0847    3 VVLDTETTGLDPaKDRIIEIG---AVKVDDGRIVETfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 187 GKVVVGH-------ALHNDFQALKYVHPRSQTRDTTYvpnfLSEPGLHTRARVSLKDLALQLlhkKIQVGQHgHSSVEDA 259
Cdd:COG0847   80 GAVLVAHnaafdlgFLNAELRRAGLPLPPFPVLDTLR----LARRLLPGLPSYSLDALCERL---GIPFDER-HRALADA 151


                 ....*...
gi 530407250 260 TTAMELYR 267
Cdd:COG0847  152 EATAELFL 159
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 111-204 3.14e-05

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 45.71  E-value: 3.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP-RG-RVSELARCSIVSyhGNVL--YDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLK 186
Cdd:PRK08074   6 VVVDLETTGNSPkKGdKIIQIAAVVVED--GEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83

                         90
                 ....*....|....*...
gi 530407250 187 GKVVVGHALHNDFQALKY 204
Cdd:PRK08074  84 GAYFVAHNVHFDLNFLNE 101
 
Name Accession Description Interval E-value
ISG20 cd06149
DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar ...
 111-267 1.31e-90

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: 267.38  E-value: 1.31e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVV 190
Cdd:cd06149    1 VAIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNATPFAVAQKEILKILKGKVV 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530407250 191 VGHALHNDFQALKYVHPRSQTRDTTYVPNFLSEPGLHTRARVSLKDLALQLLHKKIQVGQHGHSSVEDATTAMELYR 267
Cdd:cd06149   81 VGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFPENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELYK 157
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 111-267 7.96e-77

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: 7.96e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRGRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVV 190
Cdd:cd06144    1 VALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRIL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530407250 191 VGHALHNDFQALKYVHPRSQTRDT-TYVPnfLSEPGLHtrARVSLKDLALQLLHKKIQVGQhgHSSVEDATTAMELYR 267
Cdd:cd06144   81 VGHALKNDLKVLKLDHPKKLIRDTsKYKP--LRKTAKG--KSPSLKKLAKQLLGLDIQEGE--HSSVEDARAAMRLYR 152
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 111-265 1.98e-50

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: 164.20  E-value: 1.98e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGprgRVSELARCSIVSYHGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAVP-FQVAQKEILKLL-KGK 188
Cdd:cd06145    1 FALDCEMCYTT---DGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVTTtLEDVQKKLLSLIsPDT 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530407250 189 VVVGHALHNDFQALKYVHPRsqTRDTTYVpnFLSEPGLhtRARVSLKDLALQLLHKKIQVGQHGHSSVEDATTAMEL 265
Cdd:cd06145   78 ILVGHSLENDLKALKLIHPR--VIDTAIL--FPHPRGP--PYKPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALEL 148
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 111-267 1.51e-45

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: 152.05  E-value: 1.51e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRGrvSELARCSIVSY-HGNVLYDKYIRPEMPIADYRTRWSGITRQHMRKAV-----PFQ--VAQKEIL 182
Cdd:cd06137    1 VALDCEMVGLADGD--SEVVRISAVDVlTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEAAkagktIFGweAARAALW 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 183 KLLKGK-VVVGHALHNDFQALKYVHPRsqTRDTTYV-PNFLSEPGLhtRARVSLKDLALQLLHKKIQVGQHGHSSVEDAT 260
Cdd:cd06137   79 KFIDPDtILVGHSLQNDLDALRMIHTR--VVDTAILtREAVKGPLA--KRQWSLRTLCRDFLGLKIQGGGEGHDSLEDAL 154


                 ....*..
gi 530407250 261 TAMELYR 267
Cdd:cd06137  155 AAREVVL 161
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 111-274 1.36e-38

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 134.35  E-value: 1.36e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250   111 VAIDCEMVGTGPRGrvSELARCSIVSYHGN---VLYDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKG 187
Cdd:smart00479   3 VVIDCETTGLDPGK--DEIIEIAAVDVDGGeiiEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250   188 KV-VVGHALHNDFQALKYVHPR--------SQTRDT-TYVPNFLSEPGlhtraRVSLKDLALQLLHKKIqvgQHGHSSVE 257
Cdd:smart00479  81 RIlVAGNSAHFDLRFLKLEHPRlgikqppkLPVIDTlKLARATNPGLP-----KYSLKKLAKRLLLEVI---QRAHRALD 152

                          170
                   ....*....|....*..
gi 530407250   258 DATTAMELYRLVEVQWE 274
Cdd:smart00479 153 DARATAKLFKKLLERLE 169
PAN2_exo cd06143
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2; PAN2 is the catalytic ...
 111-267 3.42e-26

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: 101.92  E-value: 3.42e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP--------------RGRVSELARCSIV----SYHGNVLYDKYIRPEMPIADYRTRWSGI--------T 164
Cdd:cd06143    1 VAIDAEFVKLKPeeteirsdgtkstiRPSQMSLARVSVVrgegELEGVPFIDDYISTTEPVVDYLTRFSGIkpgdldpkT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 165 RQHmrKAVPFQVAQKEiLKLL--KGKVVVGHALHNDFQALKYVHPRSQTRDTTYVpnFLsepgLHTRARVSLKDLALQLL 242
Cdd:cd06143   81 SSK--NLTTLKSAYLK-LRLLvdLGCIFVGHGLAKDFRVINIQVPKEQVIDTVEL--FH----LPGQRKLSLRFLAWYLL 151

                        170       180
                 ....*....|....*....|....*
gi 530407250 243 HKKIQvgQHGHSSVEDATTAMELYR 267
Cdd:cd06143  152 GEKIQ--SETHDSIEDARTALKLYR 174
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 111-266 1.13e-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: 78.93  E-value: 1.13e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250  111 VAIDCEMVGTGPRG-RVSELARCSIVSY--HGNVLYDKYIRPEMP--IADYRTRWSGITRQHMRKAVPFQVAQKEILKLL 185
Cdd:pfam00929   1 VVIDLETTGLDPEKdEIIEIAAVVIDGGenEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250  186 -KGKVVVGH--------ALHNDFQALKYVHP-RSQTRDttYVPNFLSEPGLhtRARVSLKDLALQLLHKKIqvgQHGHSS 255
Cdd:pfam00929  81 rKGNLLVAHnasfdvgfLRYDDKRFLKKPMPkLNPVID--TLILDKATYKE--LPGRSLDALAEKLGLEHI---GRAHRA 153

                         170
                  ....*....|.
gi 530407250  256 VEDATTAMELY 266
Cdd:pfam00929 154 LDDARATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 111-267 2.04e-14

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: 69.64  E-value: 2.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGPRG-RVSELArcsIVSYHGNVL----YDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLL 185
Cdd:cd06127    1 VVFDTETTGLDPKKdRIIEIG---AVKVDGGIEiverFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 186 KGKVVVGHALHNDFQALKYVHPRsqtrdttYVPNFLSEPGLHTRA--------RVSLKDLALQLLHKKIQVGQHgHSSVE 257
Cdd:cd06127   78 GGRVLVAHNASFDLRFLNRELRR-------LGGPPLPNPWIDTLRlarrllpgLRSHRLGLLLAERYGIPLEGA-HRALA 149

                        170
                 ....*....|
gi 530407250 258 DATTAMELYR 267
Cdd:cd06127  150 DALATAELLL 159
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 111-267 3.95e-13

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 66.36  E-value: 3.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP-RGRVSELArcsIVSYHGNVLYDK---YIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLK 186
Cdd:COG0847    3 VVLDTETTGLDPaKDRIIEIG---AVKVDDGRIVETfhtLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 187 GKVVVGH-------ALHNDFQALKYVHPRSQTRDTTYvpnfLSEPGLHTRARVSLKDLALQLlhkKIQVGQHgHSSVEDA 259
Cdd:COG0847   80 GAVLVAHnaafdlgFLNAELRRAGLPLPPFPVLDTLR----LARRLLPGLPSYSLDALCERL---GIPFDER-HRALADA 151


                 ....*...
gi 530407250 260 TTAMELYR 267
Cdd:COG0847  152 EATAELFL 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 111-270 1.32e-06

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 47.83  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP-RGRVSELArcsIVSYHGNVL---YDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLK 186
Cdd:COG2176   11 VVFDLETTGLSPkKDEIIEIG---AVKVENGEIvdrFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 187 GKVVVGHALHNDFQALKYVHPRSQTR------DTtyVPnfLS---EPGLHtraRVSLKDLALQLlhkKIQVGQHgHSSVE 257
Cdd:COG2176   88 DAVLVAHNASFDLGFLNAALKRLGLPfdnpvlDT--LE--LArrlLPELK---SYKLDTLAERL---GIPLEDR-HRALG 156

                        170
                 ....*....|....
gi 530407250 258 DATTAMELY-RLVE 270
Cdd:COG2176  157 DAEATAELFlKLLE 170
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 111-204 3.14e-05

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 45.71  E-value: 3.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEMVGTGP-RG-RVSELARCSIVSyhGNVL--YDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLK 186
Cdd:PRK08074   6 VVVDLETTGNSPkKGdKIIQIAAVVVED--GEILerFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLE 83

                         90
                 ....*....|....*...
gi 530407250 187 GKVVVGHALHNDFQALKY 204
Cdd:PRK08074  84 GAYFVAHNVHFDLNFLNE 101
PRK06807 PRK06807
3'-5' exonuclease;
106-203 3.50e-04

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 41.72  E-value: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 106 LPSKCVAIDCEMVGTGP-RGRVSELArcsIVSYHGNVLYDKY---IRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEI 181
Cdd:PRK06807   6 LPLDYVVIDFETTGFNPyNDKIIQVA---AVKYRNHELVDQFvsyVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82

                         90       100
                 ....*....|....*....|..
gi 530407250 182 LKLLKGKVVVGHALHNDFQALK 203
Cdd:PRK06807  83 LAFLHTNVIVAHNASFDMRFLK 104
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 111-203 4.58e-04

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: 40.19  E-value: 4.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530407250 111 VAIDCEmvgTGPRGRVSElarCSI--VSYHGNVLYDKY---IRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLL 185
Cdd:cd06130    2 VAIDFE---TANADRASA---CSIglVKVRDGQIVDTFytlIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL 75

                         90
                 ....*....|....*...
gi 530407250 186 KGKVVVGHALHNDFQALK 203
Cdd:cd06130   76 GGSLVVAHNASFDRSVLR 93
polC PRK00448
DNA polymerase III PolC; Validated
 137-193 7.45e-03

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 38.28  E-value: 7.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 530407250  137 YHGNVL--YDKYIRPEMPIADYRTRWSGITRQHMRKAVPFQVAQKEILKLLKGKVVVGH 193
Cdd:PRK00448  447 KNGEIIdkFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAH 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH