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Conserved domains on  [gi|531011100|gb|EQD69566|]
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ribonuclease T, partial [mine drainage metagenome]

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 ...
 7-194 2.61e-104

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 cd06134:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 189  Bit Score: 298.44  E-value: 2.61e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   7 RFRGFLPVVVDLETGGFHAATDALLQIGAVLLECDPEGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPALPE 86
Cdd:cd06134    1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  87 EEALIRLFRLVRRALTAHSCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLLGQTVLAKAVAEIG 166
Cdd:cd06134   81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                        170       180
                 ....*....|....*....|....*...
gi 531011100 167 IPVDSGQTHQALYDAELTAQLFCRLVNR 194
Cdd:cd06134  161 IEFDNKEAHSALYDTQKTAELFCKIVNR 188
 
Name Accession Description Interval E-value
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 7-194 2.61e-104

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: 298.44  E-value: 2.61e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   7 RFRGFLPVVVDLETGGFHAATDALLQIGAVLLECDPEGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPALPE 86
Cdd:cd06134    1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  87 EEALIRLFRLVRRALTAHSCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLLGQTVLAKAVAEIG 166
Cdd:cd06134   81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                        170       180
                 ....*....|....*....|....*...
gi 531011100 167 IPVDSGQTHQALYDAELTAQLFCRLVNR 194
Cdd:cd06134  161 IEFDNKEAHSALYDTQKTAELFCKIVNR 188
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
 4-202 7.52e-95

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: 274.79  E-value: 7.52e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    4 MAERFRGFLPVVVDLETGGFHAATDALLQIGAVLLECDPEGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPA 83
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   84 LPEEEALIRLFRLVRRALTAHSCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLLGQTVLAKAVA 163
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 531011100  164 EIGIPVDSGQTHQALYDAELTAQLFCRLVNRceeWTRAG 202
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNR---WKELG 196
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 14-193 6.92e-36

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 123.75  E-value: 6.92e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVpgQTLSLEVTPFEgaHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:COG0847    3 VVLDTETTGLDPAKDRIIEIGAVKVD---DGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  94 FRLVRraltahscsRAILTGHNAFFDLGFLNAAATRSAVkrnPFHPFSTFDTVTLAGVL---LGQTVLAKAVAEIGIPVD 170
Cdd:COG0847   75 LEFLG---------GAVLVAHNAAFDLGFLNAELRRAGL---PLPPFPVLDTLRLARRLlpgLPSYSLDALCERLGIPFD 142

                        170       180
                 ....*....|....*....|...
gi 531011100 171 sgQTHQALYDAELTAQLFCRLVN 193
Cdd:COG0847  143 --ERHRALADAEATAELFLALLR 163
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 14-188 5.01e-25

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: 95.88  E-value: 5.01e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDALLQIGAVllECDPeGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAV--VIDG-GENEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   94 FRLVRRaltahscsRAILTGHNAFFDLGFLNAAATR----SAVKRNPFHPFSTFDTVTLAGvlLGQTVLAKAVAEIGIPV 169
Cdd:pfam00929  77 LEFLRK--------GNLLVAHNASFDVGFLRYDDKRflkkPMPKLNPVIDTLILDKATYKE--LPGRSLDALAEKLGLEH 146

                         170
                  ....*....|....*....
gi 531011100  170 DsGQTHQALYDAELTAQLF 188
Cdd:pfam00929 147 I-GRAHRALDDARATAKLF 164
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 14-194 1.18e-21

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 86.97  E-value: 1.18e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    14 VVVDLETGGFHAATDALLQIGAVLLecdpEGRLVpGQTLSLEVTPFEgaHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:smart00479   3 VVIDCETTGLDPGKDEIIEIAAVDV----DGGEI-IEVFDTYVKPDR--PITDYATEIHGITPEM-LDDAPTFEEVLEEL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    94 FRLVRRaltahscsRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPfsTFDTVTLAGVLLG---QTVLAKAVAEIGIPVD 170
Cdd:smart00479  75 LEFLRG--------RILVAGNSAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPglpKYSLKKLAKRLLLEVI 144

                          170       180
                   ....*....|....*....|....
gi 531011100   171 sGQTHQALYDAELTAQLFCRLVNR 194
Cdd:smart00479 145 -QRAHRALDDARATAKLFKKLLER 167
polC PRK00448
DNA polymerase III PolC; Validated
 14-197 9.71e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 72.18  E-value: 9.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLV--------PGQTLSLEVTPFegahidpealavNGIDPTHpLRPALP 85
Cdd:PRK00448  422 VVFDVETTGLSAVYDEIIEIGAVKIK---NGEIIdkfeffikPGHPLSAFTTEL------------TGITDDM-VKDAPS 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   86 EEEAL--IRLFrlvrraltahsCSRAILTGHNAFFDLGFLNAAATRSAVKR--NPFhpfstFDTVTLAGVL--------L 153
Cdd:PRK00448  486 IEEVLpkFKEF-----------CGDSILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDTLELSRFLypelkshrL 549

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 531011100  154 GqtVLAKavaEIGIPVDsgQTHQALYDAELTAQLFCRLVNRCEE 197
Cdd:PRK00448  550 N--TLAK---KFGVELE--HHHRADYDAEATAYLLIKFLKDLKE 586
 
Name Accession Description Interval E-value
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 7-194 2.61e-104

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: 298.44  E-value: 2.61e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   7 RFRGFLPVVVDLETGGFHAATDALLQIGAVLLECDPEGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPALPE 86
Cdd:cd06134    1 RFRGFLPVVVDVETGGFNPQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFNGIDPFHPFRFAVDE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  87 EEALIRLFRLVRRALTAHSCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLLGQTVLAKAVAEIG 166
Cdd:cd06134   81 KEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYGQTVLAKACQAAG 160

                        170       180
                 ....*....|....*....|....*...
gi 531011100 167 IPVDSGQTHQALYDAELTAQLFCRLVNR 194
Cdd:cd06134  161 IEFDNKEAHSALYDTQKTAELFCKIVNR 188
RNaseT TIGR01298
ribonuclease T; This model describes ribonuclease T, an enzyme found so far only in ...
 4-202 7.52e-95

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: 274.79  E-value: 7.52e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    4 MAERFRGFLPVVVDLETGGFHAATDALLQIGAVLLECDPEGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPA 83
Cdd:TIGR01298   1 LARRFRGYLPVVVDVETGGFNAATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFTGIDLDHPLRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   84 LPEEEALIRLFRLVRRALTAHSCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLLGQTVLAKAVA 163
Cdd:TIGR01298  81 VQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVARTGIKRNPFHPFSSFDTATLAGLAYGQTVLAKACQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 531011100  164 EIGIPVDSGQTHQALYDAELTAQLFCRLVNRceeWTRAG 202
Cdd:TIGR01298 161 AAGMDFDNRQAHSALYDTEKTAELFCGIVNR---WKELG 196
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 14-193 6.92e-36

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 123.75  E-value: 6.92e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVpgQTLSLEVTPFEgaHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:COG0847    3 VVLDTETTGLDPAKDRIIEIGAVKVD---DGRIV--ETFHTLVNPER--PIPPEATAIHGITDED-VADAPPFAEVLPEL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  94 FRLVRraltahscsRAILTGHNAFFDLGFLNAAATRSAVkrnPFHPFSTFDTVTLAGVL---LGQTVLAKAVAEIGIPVD 170
Cdd:COG0847   75 LEFLG---------GAVLVAHNAAFDLGFLNAELRRAGL---PLPPFPVLDTLRLARRLlpgLPSYSLDALCERLGIPFD 142

                        170       180
                 ....*....|....*....|...
gi 531011100 171 sgQTHQALYDAELTAQLFCRLVN 193
Cdd:COG0847  143 --ERHRALADAEATAELFLALLR 163
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 4-197 2.83e-32

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 114.86  E-value: 2.83e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   4 MAERFRGFLPVVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVpgQTLSLEVTPfeGAHIDPEALAVNGIDPtHPLRPA 83
Cdd:COG2176    1 MSLDLEDLTYVVFDLETTGLSPKKDEIIEIGAVKVE---NGEIV--DRFSTLVNP--GRPIPPFITELTGITD-EMVADA 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  84 LPEEEALIRLFRLVRraltahscsRAILTGHNAFFDLGFLNAAATRsaVKRNPFHPFstFDTVTLAGVLLGQT---VLAK 160
Cdd:COG2176   73 PPFEEVLPEFLEFLG---------DAVLVAHNASFDLGFLNAALKR--LGLPFDNPV--LDTLELARRLLPELksyKLDT 139

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 531011100 161 AVAEIGIPVDsgQTHQALYDAELTAQLFCRLVNRCEE 197
Cdd:COG2176  140 LAERLGIPLE--DRHRALGDAEATAELFLKLLEKLEE 174
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 14-188 5.01e-25

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: 95.88  E-value: 5.01e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDALLQIGAVllECDPeGRLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAV--VIDG-GENEIGETFHTYVKPTRLPKLTDECTKFTGITQAM-LDNKPSFEEVLEEF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   94 FRLVRRaltahscsRAILTGHNAFFDLGFLNAAATR----SAVKRNPFHPFSTFDTVTLAGvlLGQTVLAKAVAEIGIPV 169
Cdd:pfam00929  77 LEFLRK--------GNLLVAHNASFDVGFLRYDDKRflkkPMPKLNPVIDTLILDKATYKE--LPGRSLDALAEKLGLEH 146

                         170
                  ....*....|....*....
gi 531011100  170 DsGQTHQALYDAELTAQLF 188
Cdd:pfam00929 147 I-GRAHRALDDARATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 14-188 9.74e-25

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: 94.67  E-value: 9.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLecdpEGRLVPGQTLSLEVTPfeGAHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKV----DGGIEIVERFETLVNP--GRPIPPEATAIHGITDEM-LADAPPFEEVLPEF 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  94 FRLVRraltahscsRAILTGHNAFFDLGFLNAAATRSavkRNPFHPFSTFDTVTLAGVLLGQTV----LAKAVAEIGIPV 169
Cdd:cd06127   74 LEFLG---------GRVLVAHNASFDLRFLNRELRRL---GGPPLPNPWIDTLRLARRLLPGLRshrlGLLLAERYGIPL 141

                        170
                 ....*....|....*....
gi 531011100 170 DsgQTHQALYDAELTAQLF 188
Cdd:cd06127  142 E--GAHRALADALATAELL 158
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 14-194 1.18e-21

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 86.97  E-value: 1.18e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    14 VVVDLETGGFHAATDALLQIGAVLLecdpEGRLVpGQTLSLEVTPFEgaHIDPEALAVNGIDPTHpLRPALPEEEALIRL 93
Cdd:smart00479   3 VVIDCETTGLDPGKDEIIEIAAVDV----DGGEI-IEVFDTYVKPDR--PITDYATEIHGITPEM-LDDAPTFEEVLEEL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100    94 FRLVRRaltahscsRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPfsTFDTVTLAGVLLG---QTVLAKAVAEIGIPVD 170
Cdd:smart00479  75 LEFLRG--------RILVAGNSAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPglpKYSLKKLAKRLLLEVI 144

                          170       180
                   ....*....|....*....|....
gi 531011100   171 sGQTHQALYDAELTAQLFCRLVNR 194
Cdd:smart00479 145 -QRAHRALDDARATAKLFKKLLER 167
polC PRK00448
DNA polymerase III PolC; Validated
 14-197 9.71e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 72.18  E-value: 9.71e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLV--------PGQTLSLEVTPFegahidpealavNGIDPTHpLRPALP 85
Cdd:PRK00448  422 VVFDVETTGLSAVYDEIIEIGAVKIK---NGEIIdkfeffikPGHPLSAFTTEL------------TGITDDM-VKDAPS 485

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   86 EEEAL--IRLFrlvrraltahsCSRAILTGHNAFFDLGFLNAAATRSAVKR--NPFhpfstFDTVTLAGVL--------L 153
Cdd:PRK00448  486 IEEVLpkFKEF-----------CGDSILVAHNASFDVGFINTNYEKLGLEKikNPV-----IDTLELSRFLypelkshrL 549

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 531011100  154 GqtVLAKavaEIGIPVDsgQTHQALYDAELTAQLFCRLVNRCEE 197
Cdd:PRK00448  550 N--TLAK---KFGVELE--HHHRADYDAEATAYLLIKFLKDLKE 586
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 4-196 8.93e-14

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 69.21  E-value: 8.93e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   4 MAERFrgflpVVVDLETGGfHAAT--DALLQIGAVLLEcdpEGRLVpgQTLSLEVTPfeGAHIDPEALAVNGIDPtHPLR 81
Cdd:PRK08074   1 MSKRF-----VVVDLETTG-NSPKkgDKIIQIAAVVVE---DGEIL--ERFSSFVNP--ERPIPPFITELTGISE-EMVK 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  82 PALPEEEALIRLFRLVRRAltahscsraILTGHNAFFDLGFLNAAATRSAVkrNPFHpFSTFDTVTLAGVLL-GQ----- 155
Cdd:PRK08074  67 QAPLFEDVAPEIVELLEGA---------YFVAHNVHFDLNFLNEELERAGY--TEIH-CPKLDTVELARILLpTAesykl 134

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 531011100 156 TVLAKavaEIGIPVDsgQTHQALYDAELTAQLFCRLVNRCE 196
Cdd:PRK08074 135 RDLSE---ELGLEHD--QPHRADSDAEVTAELFLQLLNKLE 170
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
14-194 6.94e-11

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 60.70  E-value: 6.94e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLeCDPE--GRLvpgQTLsleVTPfeGAHIDPEALAVNGIDpTHPLRPALPEEEALI 91
Cdd:PRK07883  18 VVVDLETTGGSPAGDAITEIGAVKV-RGGEvlGEF---ATL---VNP--GRPIPPFITVLTGIT-TAMVAGAPPIEEVLP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  92 RLFRLVRraltahscsRAILTGHNAFFDLGFLNAAATRSAVkrnPFHPFSTFDTVTLA-GVLLGQTV----LAKAVAEIG 166
Cdd:PRK07883  88 AFLEFAR---------GAVLVAHNAPFDIGFLRAAAARCGY---PWPGPPVLCTVRLArRVLPRDEApnvrLSTLARLFG 155

                        170       180
                 ....*....|....*....|....*...
gi 531011100 167 IPVDSgqTHQALYDAELTAQLFCRLVNR 194
Cdd:PRK07883 156 ATTTP--THRALDDARATVDVLHGLIER 181
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 14-187 1.29e-10

DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 60.20  E-value: 1.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVpgQTLSLEVTPFEgaHIDPEALAVNGIDPTHpLRPAlPEEEALIRL 93
Cdd:TIGR01407   3 AVVDLETTGTQLSFDKIIQIGIVVVE---DGEIV--DTFHTDVNPNE--PIPPFIQELTGISDNM-LQQA-PYFSQVAQE 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   94 FRlvrraltaHSCSRAILTGHNAFFDLGFLNAAATRSAVkrnPFHPFSTFDTVTLAGVLL------GQTVLAKavaEIGI 167
Cdd:TIGR01407  74 IY--------DLLEDGIFVAHNVHFDLNFLAKALKDCGY---EPLPKPRIDTVELAQIFFpteesyQLSELSE---ALGL 139

                         170       180
                  ....*....|....*....|
gi 531011100  168 PVDsgQTHQALYDAELTAQL 187
Cdd:TIGR01407 140 THE--NPHRADSDAQATAEL 157
PRK07740 PRK07740
hypothetical protein; Provisional
 12-197 4.12e-10

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 57.37  E-value: 4.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  12 LPVVV-DLETGGFHAAT-DALLQIGAVLLEcdpeGRLVPGQTLSLEVTPfeGAHIDPEALAVNGIDpTHPLRPALPEEEA 89
Cdd:PRK07740  59 LPFVVfDLETTGFSPQQgDEILSIGAVKTK----GGEVETDTFYSLVKP--KRPIPEHILELTGIT-AEDVAFAPPLAEV 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  90 LIRLFRLVRRAltahscsraILTGHNAFFDLGFLNAAATRSAvkRNPF-HPFstFDTVTLAGVLLGQTV---LAKAVAEI 165
Cdd:PRK07740 132 LHRFYAFIGAG---------VLVAHHAGHDKAFLRHALWRTY--RQPFtHRL--IDTMFLTKLLAHERDfptLDDALAYY 198

                        170       180       190
                 ....*....|....*....|....*....|..
gi 531011100 166 GIPVDsgQTHQALYDAELTAQLFCRLVNRCEE 197
Cdd:PRK07740 199 GIPIP--RRHHALGDALMTAKLWAILLVEAQQ 228
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 14-188 1.37e-08

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: 52.84  E-value: 1.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGFHAATDaLLQIGAVLLEcdpeGRLVPGQTLSLEVTPFEGahIDPEALAVNGIDPTHpLRPAlPEEEALIRL 93
Cdd:TIGR00573  10 TTGDNETTGLYAGHD-IIEIGAVEII----NRRITGNKFHTYIKPDRP--IDPDAIKIHGITDDM-LKDK-PDFKEIAED 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   94 FRLVRRAltahscsrAILTGHNAFFDLGFLNAAATRSAVKRNPFHPF-STFDTVTLAGVLLG---QTVLAKAvAEIGIPV 169
Cdd:TIGR00573  81 FADYIRG--------AELVIHNASFDVGFLNYEFSKLYKVEPKTNDViDTTDTLQYARPEFPgkrNTLDALC-KRYEITN 151

                         170
                  ....*....|....*....
gi 531011100  170 DSGQTHQALYDAELTAQLF 188
Cdd:TIGR00573 152 SHRALHGALADAFILAKLY 170
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 85-149 2.59e-08

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.


Pssm-ID: 176647 [Multi-domain]  Cd Length: 96  Bit Score: 49.74  E-value: 2.59e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 531011100  85 PEEEALIRLFRLVRRAltahscSRAILTGHNAFFDLGFLNAAATRSAVKrNPFHPFSTFDTVTLA 149
Cdd:cd06125   27 PEDTAVIDLKDILRDK------PLAILVGHNGSFDLPFLNNRCAELGLK-YPLLAGSWIDTIKLA 84
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 14-188 4.90e-07

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: 47.91  E-value: 4.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAAT-DALLQIGAVLLECdpegRLVPGQTLSLEVTPfeGAHIDPEALAVNGIDpthplrpalpeEEALIR 92
Cdd:cd06131    2 IVLDTETTGLDPREgHRIIEIGCVELIN----RRLTGNTFHVYINP--ERDIPEEAFKVHGIT-----------DEFLAD 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  93 --LFRLVRRALTAHsCSRAILTGHNAFFDLGFLNAAATRSAVKRNPFHPFSTFDTVTLAGVLL-GQTV-LAKAVAEIGIP 168
Cdd:cd06131   65 kpKFAEIADEFLDF-IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFpGKPNsLDALCKRFGID 143

                        170       180
                 ....*....|....*....|
gi 531011100 169 VDSGQTHQALYDAELTAQLF 188
Cdd:cd06131  144 NSHRTLHGALLDAELLAEVY 163
PRK09145 PRK09145
3'-5' exonuclease;
14-124 2.31e-06

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 46.43  E-value: 2.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVPGQTLSLEVTPfeGAHIDPEALAVNGIDPtHPLRPALPEEEALIRL 93
Cdd:PRK09145  32 VALDCETTGLDPRRAEIVSIAAVKIR---GNRILTSERLELLVRP--PQSLSAESIKIHRLRH-QDLEDGLSEEEALRQL 105

                         90       100       110
                 ....*....|....*....|....*....|.
gi 531011100  94 FRLVRraltahscSRAILtGHNAFFDLGFLN 124
Cdd:PRK09145 106 LAFIG--------NRPLV-GYYLEFDVAMLN 127
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 110-190 2.19e-05

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: 42.88  E-value: 2.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100 110 ILTGHNAFFDLGFLNAAATRSAVkrnPFHPFSTFDTVTLA---GVLLGQTVLAKAVAEIGIPVdsgQTHQALYDAELTAQ 186
Cdd:cd06130   79 LVVAHNASFDRSVLRAALEAYGL---PPPPYQYLCTVRLArrvWPLLPNHKLNTVAEHLGIEL---NHHDALEDARACAE 152


                 ....
gi 531011100 187 LFCR 190
Cdd:cd06130  153 ILLA 156
PRK06807 PRK06807
3'-5' exonuclease;
14-197 2.32e-05

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 44.03  E-value: 2.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  14 VVVDLETGGFHAATDALLQIGAVLLEcdpEGRLVPgQTLSLeVTPfeGAHIDPEALAVNGID-------PThpLRPALPE 86
Cdd:PRK06807  11 VVIDFETTGFNPYNDKIIQVAAVKYR---NHELVD-QFVSY-VNP--ERPIPDRITSLTGITnyrvsdaPT--IEEVLPL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  87 EEALIRLFRLVrraltahscsrailtGHNAFFDLGFLNAAATRSAVK--RNPfhpfsTFDTVTLAGVLLGQTV---LAKA 161
Cdd:PRK06807  82 FLAFLHTNVIV---------------AHNASFDMRFLKSNVNMLGLPepKNK-----VIDTVFLAKKYMKHAPnhkLETL 141

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 531011100 162 VAEIGIPVDSgqtHQALYDAELTAQLFCRLVNRCEE 197
Cdd:PRK06807 142 KRMLGIRLSS---HNAFDDCITCAAVYQKCASIEEE 174
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 17-184 1.00e-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: 41.48  E-value: 1.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  17 DLETGGFHAATDALLQIGAVllECDPEgrLVPGQTLSLEVTPFEGAHIDPEALAVNGIDPTHPLRPALPEEEALIRLFRL 96
Cdd:cd06138    4 DYETFGLNPSFDQILQFAAI--RTDEN--FNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEGLSEYEFIAKIHRL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100  97 VrraLTAHSCSrailTGHNAF-FDLGFlnaaaTRSAVKRNPFHPF--------STFD--TVTLAGVLLGQTVLAKAVAEI 165
Cdd:cd06138   80 F---NTPGTCI----VGYNNIrFDDEF-----LRFAFYRNLYDPYtwewkngnSRWDllDVVRAYYALRPDGIVWPKNDD 147

                        170       180       190
                 ....*....|....*....|....*....|.
gi 531011100 166 GIPV------------DSGQTHQALYDAELT 184
Cdd:cd06138  148 GKPSfkledlaqangiEHSNAHDALSDVEAT 178
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 14-189 7.91e-04

3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides.


Pssm-ID: 406788  Cd Length: 177  Bit Score: 38.95  E-value: 7.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   14 VVVDLETGGfHAATDALLQIGAVLLECDpEGRLvpGQTlslevtpFEGAhIDPEALAVNGIDPT-----------HPLRP 82
Cdd:pfam16473   3 LMIDIETLG-NEPTAPIVSIGAVFFDPE-TGEL--GKE-------FYAR-IDLESSMSAGATIDadtilwwlkqsSEARA 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 531011100   83 AL------PEEEALIRLFRLVRRALTAHScsrAILTGHNAFFDLGFLNAAATRSAVKRnPFHPFSTFDTVTLagVLLGQT 156
Cdd:pfam16473  71 QLlgddapSLPDALLDLNDFIRDNGDPKS---LKVWGNGASFDNVILRAAFERGGLPA-PWKYWNDRDVRTI--VALGPE 144

                         170       180       190
                  ....*....|....*....|....*....|...
gi 531011100  157 VLAKAVAEIGIPvdsGQTHQALYDAELTAQLFC 189
Cdd:pfam16473 145 LGYDPKRDIPFE---GVKHNALDDAIHQAKYVS 174
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 154-191 6.40e-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: 36.04  E-value: 6.40e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 531011100 154 GQTVLAKAVAEIGIPVDsGQTHQALYDAELTAQLFCRL 191
Cdd:cd06133  139 KRTGLSKALEYLGLEFE-GRHHRGLDDARNIARILKRL 175
 
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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