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Conserved domains on  [gi|2087638991|dbj|GJG70182|]
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ribonuclease T [Enterobacter hormaechei]

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 ...
10-209 6.64e-132

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 TIGR01298:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 200  Bit Score: 369.16  E-value: 6.64e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  10 LCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGA 89
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  90 VSEYEALHAIFKMVRKGMKENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALSGLALGQTVLSKACI 169
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2087638991 170 TAGIAFDGTQAHSALYDTERTAELFCEIVNRWKRLGGWPL 209
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNRWKELGGWPP 200
 
Name Accession Description Interval E-value
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
10-209 6.64e-132

ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. [Transcription, RNA processing]


Pssm-ID: 188129 [Multi-domain]  Cd Length: 200  Bit Score: 369.16  E-value: 6.64e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  10 LCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGA 89
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  90 VSEYEALHAIFKMVRKGMKENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALSGLALGQTVLSKACI 169
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2087638991 170 TAGIAFDGTQAHSALYDTERTAELFCEIVNRWKRLGGWPL 209
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNRWKELGGWPP 200
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
13-201 2.27e-130

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. 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. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 364.69  E-value: 2.27e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  13 RFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGAVSE 92
Cdd:cd06134     1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  93 YEALHAIFKMVRKGMKENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALSGLALGQTVLSKACITAG 172
Cdd:cd06134    81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160
                         170       180
                  ....*....|....*....|....*....
gi 2087638991 173 IAFDGTQAHSALYDTERTAELFCEIVNRW 201
Cdd:cd06134   161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
20-199 8.59e-41

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 136.46  E-value: 8.59e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLkmdEQGWLVpdTTLHFHVEPFEgaNLQPEALAFNGIDPTNpLRGAVSEYEALHAI 99
Cdd:COG0847     3 VVLDTETTGLDPAKDRIIEIGAVKV---DDGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRKgmkendcsrAIMVAHNATFDHSFTMAAAERASLKRNPFHpfvTFDTAALSGLA---LGQTVLSKACITAGIAFD 176
Cdd:COG0847    75 LEFLGG---------AVLVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLlpgLPSYSLDALCERLGIPFD 142
                         170       180
                  ....*....|....*....|...
gi 2087638991 177 GtqAHSALYDTERTAELFCEIVN 199
Cdd:COG0847   143 E--RHRALADAEATAELFLALLR 163
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
20-194 2.40e-33

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: 117.45  E-value: 2.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLKMDEqgwLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNpLRGAVSEYEALHAI 99
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGE---NEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRKGMkendcsraIMVAHNATFDHSFTMAAAERASL----KRNPFHPFVTFDTAALSGLAlgQTVLSKACITAGIAF 175
Cdd:pfam00929  77 LEFLRKGN--------LLVAHNASFDVGFLRYDDKRFLKkpmpKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEH 146
                         170
                  ....*....|....*....
gi 2087638991 176 DGTqAHSALYDTERTAELF 194
Cdd:pfam00929 147 IGR-AHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
18-202 1.19e-28

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 105.46  E-value: 1.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   18 YPVVIDVETAGFNAKTDALLEIAAITLKMDEqgwlvPDTTLHFHVEPFEgaNLQPEALAFNGIDPtNPLRGAVSEYEALH 97
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-----IIEVFDTYVKPDR--PITDYATEIHGITP-EMLDDAPTFEEVLE 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   98 AIFKMVRKGmkendcsraIMVAHN-ATFDHSFTMAAAERASLKRNPFHPfvTFDTAALSGL---ALGQTVLSKACITAGI 173
Cdd:smart00479  73 ELLEFLRGR---------ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARAtnpGLPKYSLKKLAKRLLL 141
                          170       180
                   ....*....|....*....|....*....
gi 2087638991  174 AFDGTqAHSALYDTERTAELFCEIVNRWK 202
Cdd:smart00479 142 EVIQR-AHRALDDARATAKLFKKLLERLE 169
polC PRK00448
DNA polymerase III PolC; Validated
20-194 5.81e-13

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 67.17  E-value: 5.81e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   20 VVIDVETAGFNAKTDALLEIAAITLKMDEQgwlvpdttlhfhVEPFEganlqpealAFngIDPTNPL------------- 86
Cdd:PRK00448   422 VVFDVETTGLSAVYDEIIEIGAVKIKNGEI------------IDKFE---------FF--IKPGHPLsaftteltgitdd 478
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   87 --RGAVSEYEALHAIFKMvrkgmkendCSRAIMVAHNATFDHSFTMAAAERASLKR--NPFhpfvtFDTaalsgLALGQT 162
Cdd:PRK00448   479 mvKDAPSIEEVLPKFKEF---------CGDSILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDT-----LELSRF 539
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 2087638991  163 V--------LSKACITAGIAFDgtQAHSALYDTERTAELF 194
Cdd:PRK00448   540 LypelkshrLNTLAKKFGVELE--HHHRADYDAEATAYLL 577
 
Name Accession Description Interval E-value
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
10-209 6.64e-132

ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. [Transcription, RNA processing]


Pssm-ID: 188129 [Multi-domain]  Cd Length: 200  Bit Score: 369.16  E-value: 6.64e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  10 LCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGA 89
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  90 VSEYEALHAIFKMVRKGMKENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALSGLALGQTVLSKACI 169
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2087638991 170 TAGIAFDGTQAHSALYDTERTAELFCEIVNRWKRLGGWPL 209
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNRWKELGGWPP 200
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
13-201 2.27e-130

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. 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. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 364.69  E-value: 2.27e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  13 RFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEQGWLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGAVSE 92
Cdd:cd06134     1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  93 YEALHAIFKMVRKGMKENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALSGLALGQTVLSKACITAG 172
Cdd:cd06134    81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160
                         170       180
                  ....*....|....*....|....*....
gi 2087638991 173 IAFDGTQAHSALYDTERTAELFCEIVNRW 201
Cdd:cd06134   161 IEFDNKEAHSALYDTQKTAELFCKIVNRW 189
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
20-199 8.59e-41

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 136.46  E-value: 8.59e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLkmdEQGWLVpdTTLHFHVEPFEgaNLQPEALAFNGIDPTNpLRGAVSEYEALHAI 99
Cdd:COG0847     3 VVLDTETTGLDPAKDRIIEIGAVKV---DDGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRKgmkendcsrAIMVAHNATFDHSFTMAAAERASLKRNPFHpfvTFDTAALSGLA---LGQTVLSKACITAGIAFD 176
Cdd:COG0847    75 LEFLGG---------AVLVAHNAAFDLGFLNAELRRAGLPLPPFP---VLDTLRLARRLlpgLPSYSLDALCERLGIPFD 142
                         170       180
                  ....*....|....*....|...
gi 2087638991 177 GtqAHSALYDTERTAELFCEIVN 199
Cdd:COG0847   143 E--RHRALADAEATAELFLALLR 163
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
20-194 2.40e-33

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: 117.45  E-value: 2.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLKMDEqgwLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNpLRGAVSEYEALHAI 99
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGE---NEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRKGMkendcsraIMVAHNATFDHSFTMAAAERASL----KRNPFHPFVTFDTAALSGLAlgQTVLSKACITAGIAF 175
Cdd:pfam00929  77 LEFLRKGN--------LLVAHNASFDVGFLRYDDKRFLKkpmpKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEH 146
                         170
                  ....*....|....*....
gi 2087638991 176 DGTqAHSALYDTERTAELF 194
Cdd:pfam00929 147 IGR-AHRALDDARATAKLF 164
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
20-205 1.41e-29

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 108.31  E-value: 1.41e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAItlKMDeqGWLVPDtTLHFHVEPfeGANLQPEALAFNGIDPtNPLRGAVSEYEALHAI 99
Cdd:COG2176    11 VVFDLETTGLSPKKDEIIEIGAV--KVE--NGEIVD-RFSTLVNP--GRPIPPFITELTGITD-EMVADAPPFEEVLPEF 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRkgmkenDCsraIMVAHNATFDHSFTMAAAERASLK-RNPFhpfvtFDTAALSGLALGQT---VLSKACITAGIAF 175
Cdd:COG2176    83 LEFLG------DA---VLVAHNASFDLGFLNAALKRLGLPfDNPV-----LDTLELARRLLPELksyKLDTLAERLGIPL 148
                         170       180       190
                  ....*....|....*....|....*....|
gi 2087638991 176 DgtQAHSALYDTERTAELFCEIVNRWKRLG 205
Cdd:COG2176   149 E--DRHRALGDAEATAELFLKLLEKLEEKG 176
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
18-202 1.19e-28

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 105.46  E-value: 1.19e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   18 YPVVIDVETAGFNAKTDALLEIAAITLKMDEqgwlvPDTTLHFHVEPFEgaNLQPEALAFNGIDPtNPLRGAVSEYEALH 97
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGE-----IIEVFDTYVKPDR--PITDYATEIHGITP-EMLDDAPTFEEVLE 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   98 AIFKMVRKGmkendcsraIMVAHN-ATFDHSFTMAAAERASLKRNPFHPfvTFDTAALSGL---ALGQTVLSKACITAGI 173
Cdd:smart00479  73 ELLEFLRGR---------ILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARAtnpGLPKYSLKKLAKRLLL 141
                          170       180
                   ....*....|....*....|....*....
gi 2087638991  174 AFDGTqAHSALYDTERTAELFCEIVNRWK 202
Cdd:smart00479 142 EVIQR-AHRALDDARATAKLFKKLLERLE 169
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
20-194 2.16e-21

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: 86.59  E-value: 2.16e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLKmdeqGWLVPDTTLHFHVEPfeGANLQPEALAFNGIDPTnPLRGAVSEYEALHAI 99
Cdd:cd06127     1 VVFDTETTGLDPKKDRIIEIGAVKVD----GGIEIVERFETLVNP--GRPIPPEATAIHGITDE-MLADAPPFEEVLPEF 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRkgmkendcsRAIMVAHNATFDHSFTMAAAERASLkrnPFHPFVTFDTAALSGLALGQTVLSK--ACITAGIAFDG 177
Cdd:cd06127    74 LEFLG---------GRVLVAHNASFDLRFLNRELRRLGG---PPLPNPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPL 141
                         170
                  ....*....|....*..
gi 2087638991 178 TQAHSALYDTERTAELF 194
Cdd:cd06127   142 EGAHRALADALATAELL 158
polC PRK00448
DNA polymerase III PolC; Validated
20-194 5.81e-13

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 67.17  E-value: 5.81e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   20 VVIDVETAGFNAKTDALLEIAAITLKMDEQgwlvpdttlhfhVEPFEganlqpealAFngIDPTNPL------------- 86
Cdd:PRK00448   422 VVFDVETTGLSAVYDEIIEIGAVKIKNGEI------------IDKFE---------FF--IKPGHPLsaftteltgitdd 478
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   87 --RGAVSEYEALHAIFKMvrkgmkendCSRAIMVAHNATFDHSFTMAAAERASLKR--NPFhpfvtFDTaalsgLALGQT 162
Cdd:PRK00448   479 mvKDAPSIEEVLPKFKEF---------CGDSILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDT-----LELSRF 539
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 2087638991  163 V--------LSKACITAGIAFDgtQAHSALYDTERTAELF 194
Cdd:PRK00448   540 LypelkshrLNTLAKKFGVELE--HHHRADYDAEATAYLL 577
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
12-210 6.05e-08

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 52.26  E-value: 6.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  12 DRFrgfypVVIDVETAGfNA--KTDALLEIAAITLKMDEQgwlvpdttlhfhVEPFeGANLQPEAL--AF----NGIDPt 83
Cdd:PRK08074    3 KRF-----VVVDLETTG-NSpkKGDKIIQIAAVVVEDGEI------------LERF-SSFVNPERPipPFitelTGISE- 62
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  84 nplrGAVSEYEALHAIFKMVrKGMKENdcsrAIMVAHNATFDHSFTMAAAERASLkrNPFH-PfvTFDTAALS------- 155
Cdd:PRK08074   63 ----EMVKQAPLFEDVAPEI-VELLEG----AYFVAHNVHFDLNFLNEELERAGY--TEIHcP--KLDTVELArillpta 129
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2087638991 156 -GLALGQtvLSKAcitagIAFDGTQAHSALYDTERTAELFCEIVNRWKRLggwPLP 210
Cdd:PRK08074  130 eSYKLRD--LSEE-----LGLEHDQPHRADSDAEVTAELFLQLLNKLERL---PLV 175
PRK07740 PRK07740
hypothetical protein; Provisional
1-205 4.54e-07

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 48.90  E-value: 4.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991   1 MSDNAQFTGLCDRFRGFYPVVIDVETAGFN-AKTDALLEIAAITLKmdeqGWLVPDTTLHFHVEPfeGANLQPEALAFNG 79
Cdd:PRK07740   43 QKEAKRDDVLDIPLTDLPFVVFDLETTGFSpQQGDEILSIGAVKTK----GGEVETDTFYSLVKP--KRPIPEHILELTG 116
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  80 IdpTNP-LRGAVSEYEALHAIFKMVRkgmkendcsRAIMVAHNATFDHSFTMAAAERASlkRNPF-HPFVtfDTAALSGL 157
Cdd:PRK07740  117 I--TAEdVAFAPPLAEVLHRFYAFIG---------AGVLVAHHAGHDKAFLRHALWRTY--RQPFtHRLI--DTMFLTKL 181
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2087638991 158 --ALGQTV-LSKACITAGIAFdgTQAHSALYDTERTAELFCEIVNRWKRLG 205
Cdd:PRK07740  182 laHERDFPtLDDALAYYGIPI--PRRHHALGDALMTAKLWAILLVEAQQRG 230
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
20-197 9.31e-07

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: 47.83  E-value: 9.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDaLLEIAAITlKMDEQGwlvpdTTLHFHVEPFEGANLQPEALAFNGIDPtNPLRGAVSEYEALHAI 99
Cdd:TIGR00573  10 TTGDNETTGLYAGHD-IIEIGAVE-IINRRI-----TGNKFHTYIKPDRPIDPDAIKIHGITD-DMLKDKPDFKEIAEDF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991 100 FKMVRKgmkendcsrAIMVAHNATFDHSFTMAAAERASLKRNPFHPFV-TFDTA--ALSGLALGQTVLSKACITAGIafd 176
Cdd:TIGR00573  82 ADYIRG---------AELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIdTTDTLqyARPEFPGKRNTLDALCKRYEI--- 149
                         170       180
                  ....*....|....*....|.
gi 2087638991 177 gTQAHSALYDTERTAELFCEI 197
Cdd:TIGR00573 150 -TNSHRALHGALADAFILAKL 169
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
20-196 8.98e-06

DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme 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: 99835 [Multi-domain]  Cd Length: 167  Bit Score: 44.45  E-value: 8.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKT-DALLEIAAITLkMDEQgwlVPDTTLHFHVEPfeGANLQPEALAFNGIDptnplrgavSEYEALHA 98
Cdd:cd06131     2 IVLDTETTGLDPREgHRIIEIGCVEL-INRR---LTGNTFHVYINP--ERDIPEEAFKVHGIT---------DEFLADKP 66
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  99 IFKMVRKGMkENDCSRAIMVAHNATFDHSFTMAAAERASLKRNPFHPFVTFDTAALS-GLALGQTV-LSKACITAGIAFD 176
Cdd:cd06131    67 KFAEIADEF-LDFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALArKKFPGKPNsLDALCKRFGIDNS 145
                         170       180
                  ....*....|....*....|
gi 2087638991 177 GTQAHSALYDTERTAELFCE 196
Cdd:cd06131   146 HRTLHGALLDAELLAEVYLE 165
PRK06807 PRK06807
3'-5' exonuclease;
20-128 4.73e-05

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 43.26  E-value: 4.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLKMDEqgwlVPDTTLHFhVEPfeGANLQPEALAFNGIdpTNPLrgaVSEYEALHAI 99
Cdd:PRK06807   11 VVIDFETTGFNPYNDKIIQVAAVKYRNHE----LVDQFVSY-VNP--ERPIPDRITSLTGI--TNYR---VSDAPTIEEV 78
                          90       100
                  ....*....|....*....|....*....
gi 2087638991 100 FKMVRKGMKENdcsraIMVAHNATFDHSF 128
Cdd:PRK06807   79 LPLFLAFLHTN-----VIVAHNASFDMRF 102
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
20-196 2.92e-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: 39.80  E-value: 2.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  20 VVIDVETAgfNAKTDALLEIAAITLK----MDEQGWLV-PDTTlhfhvepFEGANLQpealaFNGIDPTNpLRGAVSEYE 94
Cdd:cd06130     2 VAIDFETA--NADRASACSIGLVKVRdgqiVDTFYTLIrPPTR-------FDPFNIA-----IHGITPED-VADAPTFPE 66
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  95 ALHAIFKMVrkgmkendcSRAIMVAHNATFDHSFTMAAAERASLkrnPFHPFVTFDTAALS---GLALGQTVLSKACITA 171
Cdd:cd06130    67 VWPEIKPFL---------GGSLVVAHNASFDRSVLRAALEAYGL---PPPPYQYLCTVRLArrvWPLLPNHKLNTVAEHL 134
                         170       180
                  ....*....|....*....|....*
gi 2087638991 172 GIAFdgtQAHSALYDTERTAELFCE 196
Cdd:cd06130   135 GIEL---NHHDALEDARACAEILLA 156
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
17-193 3.85e-04

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 39.94  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  17 FYpvviDVETAGFNAKTDALLEIAAItlKMDEQgwLVPDTTLHFHVEPFEGANLQPEALAFNGIDPTNPLRGAVSEYEA- 95
Cdd:cd06138     2 FY----DYETFGLNPSFDQILQFAAI--RTDEN--FNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFi 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2087638991  96 --LHAIFkmvrkgMKENDCsraIMVAHNATFDHSFTmaaaeRASLKRNPFHPF---------------VTFDTAAL--SG 156
Cdd:cd06138    74 akIHRLF------NTPGTC---IVGYNNIRFDDEFL-----RFAFYRNLYDPYtwewkngnsrwdlldVVRAYYALrpDG 139
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2087638991 157 L-----ALGQTVLSKACITAGIAFDGTQAHSALYDTERTAEL 193
Cdd:cd06138   140 IvwpknDDGKPSFKLEDLAQANGIEHSNAHDALSDVEATIAL 181
PRK09145 PRK09145
3'-5' exonuclease;
20-98 2.20e-03

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 37.96  E-value: 2.20e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2087638991  20 VVIDVETAGFNAKTDALLEIAAITLKMDEqgwLVPDTTLHFHVEPfeGANLQPEALAFNGIDPTNpLRGAVSEYEALHA 98
Cdd:PRK09145   32 VALDCETTGLDPRRAEIVSIAAVKIRGNR---ILTSERLELLVRP--PQSLSAESIKIHRLRHQD-LEDGLSEEEALRQ 104
 
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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