NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|881048170|ref|WP_048766686|]
View 

DNA polymerase III subunit epsilon [Oligella urethralis]

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 ...
 1-234 7.81e-120

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 PRK05711:

Pssm-ID: 447876 [Multi-domain]  Cd Length: 240  Bit Score: 340.68  E-value: 7.81e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   1 MRQIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADY 80
Cdd:PRK05711   4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  81 LSGAELLIHNAAFDVGFLNAEFAR--YQIPALEEIaAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDA 158
Cdd:PRK05711  84 IRGAELIIHNAPFDIGFMDYEFALlgRDIPKTNTF-CKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881048170 159 ELLADVWLAMTREQFGLLDALQDEPQIQAADAVVAAPVVGSFSLPIIRADAEELAEHAAYVEVLDKAvEGESLWHR 234
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKK-GGSCLWRK 237
 
Name Accession Description Interval E-value
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 1-234 7.81e-120

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 340.68  E-value: 7.81e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   1 MRQIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADY 80
Cdd:PRK05711   4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  81 LSGAELLIHNAAFDVGFLNAEFAR--YQIPALEEIaAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDA 158
Cdd:PRK05711  84 IRGAELIIHNAPFDIGFMDYEFALlgRDIPKTNTF-CKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881048170 159 ELLADVWLAMTREQFGLLDALQDEPQIQAADAVVAAPVVGSFSLPIIRADAEELAEHAAYVEVLDKAvEGESLWHR 234
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKK-GGSCLWRK 237
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 3-169 4.79e-94

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: 272.87  E-value: 4.79e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   3 QIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLS 82
Cdd:cd06131    1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  83 GAELLIHNAAFDVGFLNAEFARYQIPALEEIAAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDAELLA 162
Cdd:cd06131   81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLA 160


                 ....*..
gi 881048170 163 DVWLAMT 169
Cdd:cd06131  161 EVYLELT 167
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 2-224 2.89e-89

DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130473 [Multi-domain]  Cd Length: 225  Bit Score: 262.72  E-value: 2.89e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    2 RQIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:TIGR01406   1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   82 SGAELLIHNAAFDVGFLNAEFARYQiPALEEI--AAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDAE 159
Cdd:TIGR01406  81 GGSELVIHNAAFDVGFLNYELERLG-PTIKKIgeFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 881048170  160 LLADVWLAMTREQFGLLDALQDEPQIQAADAVVAAPVVGSfSLPIIRADAEELAEHAAYVEVLDK 224
Cdd:TIGR01406 160 LLAEVYLALTGGQESLLELAESNSGEAAKPSKSAEMKLGA-TLRVLAPREAELQAHEAYLDKLLK 223
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-170 2.43e-61

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 189.62  E-value: 2.43e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   2 RQIVLDTETTGMDAHQgDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:COG0847    1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  82 SGAELLIHNAAFDVGFLNAEFARYQIPALEeiaAKITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvlHGALLDAEL 160
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAEA 153

                        170
                 ....*....|
gi 881048170 161 LADVWLAMTR 170
Cdd:COG0847  154 TAELFLALLR 163
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-171 8.56e-39

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 132.42  E-value: 8.56e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170     2 RQIVLDTETTGMDaHQGDRIIEIGCIELVNREpTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:smart00479   1 TLVVIDCETTGLD-PGKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    82 SGAELLIHN-AAFDVGFLNAEFARYQIPALEEIAakITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvLHGALLDAE 159
Cdd:smart00479  79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155

                          170
                   ....*....|..
gi 881048170   160 LLADVWLAMTRE 171
Cdd:smart00479 156 ATAKLFKKLLER 167
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-164 9.28e-29

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: 106.28  E-value: 9.28e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    4 IVLDTETTGMDAhQGDRIIEIGCIELVNRE-PTGNNLHLYFNPERES--DPGALAVHGLTTEFLSQFNTFDQHAQEIADY 80
Cdd:pfam00929   1 VVIDLETTGLDP-EKDEIIEIAAVVIDGGEnEIGETFHTYVKPTRLPklTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   81 L-SGAELLIHNAAFDVGFLNAEFARYqIPALEEIAAKITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvLHGALLDA 158
Cdd:pfam00929  80 LrKGNLLVAHNASFDVGFLRYDDKRF-LKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGR-AHRALDDA 157


                  ....*.
gi 881048170  159 ELLADV 164
Cdd:pfam00929 158 RATAKL 163
 
Name Accession Description Interval E-value
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 1-234 7.81e-120

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 340.68  E-value: 7.81e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   1 MRQIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADY 80
Cdd:PRK05711   4 MRQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  81 LSGAELLIHNAAFDVGFLNAEFAR--YQIPALEEIaAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDA 158
Cdd:PRK05711  84 IRGAELIIHNAPFDIGFMDYEFALlgRDIPKTNTF-CKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDA 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 881048170 159 ELLADVWLAMTREQFGLLDALQDEPQIQAADAVVAAPVVGSFSLPIIRADAEELAEHAAYVEVLDKAvEGESLWHR 234
Cdd:PRK05711 163 EILAEVYLAMTGGQTSLGFAMEGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDKK-GGSCLWRK 237
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 3-169 4.79e-94

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: 272.87  E-value: 4.79e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   3 QIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLS 82
Cdd:cd06131    1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  83 GAELLIHNAAFDVGFLNAEFARYQIPALEEIAAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDAELLA 162
Cdd:cd06131   81 GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLA 160


                 ....*..
gi 881048170 163 DVWLAMT 169
Cdd:cd06131  161 EVYLELT 167
dnaQ_proteo TIGR01406
DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA ...
 2-224 2.89e-89

DNA polymerase III, epsilon subunit, Proteobacterial; This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130473 [Multi-domain]  Cd Length: 225  Bit Score: 262.72  E-value: 2.89e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    2 RQIVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:TIGR01406   1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDFI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   82 SGAELLIHNAAFDVGFLNAEFARYQiPALEEI--AAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALLDAE 159
Cdd:TIGR01406  81 GGSELVIHNAAFDVGFLNYELERLG-PTIKKIgeFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 881048170  160 LLADVWLAMTREQFGLLDALQDEPQIQAADAVVAAPVVGSfSLPIIRADAEELAEHAAYVEVLDK 224
Cdd:TIGR01406 160 LLAEVYLALTGGQESLLELAESNSGEAAKPSKSAEMKLGA-TLRVLAPREAELQAHEAYLDKLLK 223
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-170 2.43e-61

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 189.62  E-value: 2.43e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   2 RQIVLDTETTGMDAHQgDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:COG0847    1 RFVVLDTETTGLDPAK-DRIIEIGAVKVDDGRIV-ETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  82 SGAELLIHNAAFDVGFLNAEFARYQIPALEeiaAKITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvlHGALLDAEL 160
Cdd:COG0847   79 GGAVLVAHNAAFDLGFLNAELRRAGLPLPP---FPVLDTLRLARRLLPGlPSYSLDALCERLGIPFDER--HRALADAEA 153

                        170
                 ....*....|
gi 881048170 161 LADVWLAMTR 170
Cdd:COG0847  154 TAELFLALLR 163
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 2-172 9.46e-53

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: 169.55  E-value: 9.46e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    2 RQIVLDTETTGMDA----HQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEI 77
Cdd:TIGR00573   2 RQLVLDTETTGDNEttglYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   78 ADYLSGAELLIHNAAFDVGFLNAEFAR-YQIPALEEIAAKITDTLALARAKFPGQRNSLDALCDRLGVSNEHRVLHGALL 156
Cdd:TIGR00573  82 ADYIRGAELVIHNASFDVGFLNYEFSKlYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALA 161

                         170
                  ....*....|....*.
gi 881048170  157 DAELLADVWLAMTREQ 172
Cdd:TIGR00573 162 DAFILAKLYLVMTGKQ 177
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 4-168 2.13e-39

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 134.12  E-value: 2.13e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQgDRIIEIGCIELVNREPTGNnLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSG 83
Cdd:COG2176   11 VVFDLETTGLSPKK-DEIIEIGAVKVENGEIVDR-FSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  84 AELLIHNAAFDVGFLNAEFARYQIPaleeIAAKITDTLALARAKFPGQRN-SLDALCDRLGVSNEHRvlHGALLDAELLA 162
Cdd:COG2176   89 AVLVAHNASFDLGFLNAALKRLGLP----FDNPVLDTLELARRLLPELKSyKLDTLAERLGIPLEDR--HRALGDAEATA 162


                 ....*.
gi 881048170 163 DVWLAM 168
Cdd:COG2176  163 ELFLKL 168
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-166 4.82e-39

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: 132.42  E-value: 4.82e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAhQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSG 83
Cdd:cd06127    1 VVFDTETTGLDP-KKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  84 AELLIHNAAFDVGFLNAEFARYQIPALEeiaAKITDTLALARAKFPGQRNSL--DALCDRLGVSNEHRvlHGALLDAELL 161
Cdd:cd06127   80 RVLVAHNASFDLRFLNRELRRLGGPPLP---NPWIDTLRLARRLLPGLRSHRlgLLLAERYGIPLEGA--HRALADALAT 154


                 ....*
gi 881048170 162 ADVWL 166
Cdd:cd06127  155 AELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 2-171 8.56e-39

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 132.42  E-value: 8.56e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170     2 RQIVLDTETTGMDaHQGDRIIEIGCIELVNREpTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:smart00479   1 TLVVIDCETTGLD-PGKDEIIEIAAVDVDGGE-IIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    82 SGAELLIHN-AAFDVGFLNAEFARYQIPALEEIAakITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvLHGALLDAE 159
Cdd:smart00479  79 RGRILVAGNsAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLKLARATNPGlPKYSLKKLAKRLLLEVIQR-AHRALDDAR 155

                          170
                   ....*....|..
gi 881048170   160 LLADVWLAMTRE 171
Cdd:smart00479 156 ATAKLFKKLLER 167
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-164 9.28e-29

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: 106.28  E-value: 9.28e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    4 IVLDTETTGMDAhQGDRIIEIGCIELVNRE-PTGNNLHLYFNPERES--DPGALAVHGLTTEFLSQFNTFDQHAQEIADY 80
Cdd:pfam00929   1 VVIDLETTGLDP-EKDEIIEIAAVVIDGGEnEIGETFHTYVKPTRLPklTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   81 L-SGAELLIHNAAFDVGFLNAEFARYqIPALEEIAAKITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvLHGALLDA 158
Cdd:pfam00929  80 LrKGNLLVAHNASFDVGFLRYDDKRF-LKKPMPKLNPVIDTLILDKATYKElPGRSLDALAEKLGLEHIGR-AHRALDDA 157


                  ....*.
gi 881048170  159 ELLADV 164
Cdd:pfam00929 158 RATAKL 163
polC PRK00448
DNA polymerase III PolC; Validated
 5-171 6.48e-23

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 96.83  E-value: 6.48e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170    5 VLDTETTGMDAhQGDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGA 84
Cdd:PRK00448  423 VFDVETTGLSA-VYDEIIEIGAVKIKNGEII-DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDS 500

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   85 ELLIHNAAFDVGFLNAEFARYQIPALEEIaakITDTLALARAKFPGQRN-SLDALCDRLGVS--NEHRvlhgALLDAELL 161
Cdd:PRK00448  501 ILVAHNASFDVGFINTNYEKLGLEKIKNP---VIDTLELSRFLYPELKShRLNTLAKKFGVEleHHHR----ADYDAEAT 573

                         170
                  ....*....|
gi 881048170  162 ADVWLAMTRE 171
Cdd:PRK00448  574 AYLLIKFLKD 583
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-185 4.41e-22

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 94.25  E-value: 4.41e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   1 MRQIVLDTETTGMDAHQGDRIIEIGCI-----ELVNREPTgnnlhlYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQ 75
Cdd:PRK08074   3 KRFVVVDLETTGNSPKKGDKIIQIAAVvvedgEILERFSS------FVNPERPIPPFITELTGISEEMVKQAPLFEDVAP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  76 EIADYLSGAELLIHNAAFDVGFLNAEFARYQIPaleEIAAKITDTLALARAKFPGQRN-SLDALCDRLGVsnEHRVLHGA 154
Cdd:PRK08074  77 EIVELLEGAYFVAHNVHFDLNFLNEELERAGYT---EIHCPKLDTVELARILLPTAESyKLRDLSEELGL--EHDQPHRA 151

                        170       180       190
                 ....*....|....*....|....*....|.
gi 881048170 155 LLDAELLADVWLAmtreqfgLLDALQDEPQI 185
Cdd:PRK08074 152 DSDAEVTAELFLQ-------LLNKLERLPLV 175
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 44-159 8.54e-19

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: 79.86  E-value: 8.54e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  44 NPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGAELLIHNAAFDVGFLNAEFARYQIPALEEIAAkitDTLAL 123
Cdd:cd06130   38 RPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYL---CTVRL 114

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 881048170 124 ARAKFPGQRN-SLDALCDRLGVSNEHrvlHGALLDAE 159
Cdd:cd06130  115 ARRVWPLLPNhKLNTVAEHLGIELNH---HDALEDAR 148
PRK06063 PRK06063
DEDDh family exonuclease;
5-164 1.57e-16

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 77.05  E-value: 1.57e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   5 VLDTETTGMDAHQgDRIIEIGCIELVNREPTGNNLHLYFNPEResDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGA 84
Cdd:PRK06063  19 VVDVETSGFRPGQ-ARIISLAVLGLDADGNVEQSVVTLLNPGV--DPGPTHVHGLTAEMLEGQPQFADIAGEVAELLRGR 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  85 ELLIHNAAFDVGFLNAEFARY--QIPALEEIAakitdTLALARA-KFPGQRNSLDALCDRLGVSnEHRVlHGALLDAELL 161
Cdd:PRK06063  96 TLVAHNVAFDYSFLAAEAERAgaELPVDQVMC-----TVELARRlGLGLPNLRLETLAAHWGVP-QQRP-HDALDDARVL 168


                 ...
gi 881048170 162 ADV 164
Cdd:PRK06063 169 AGI 171
PRK07740 PRK07740
hypothetical protein; Provisional
 4-165 4.80e-16

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 74.71  E-value: 4.80e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLsqfntfdQHAQEIAD---- 79
Cdd:PRK07740  62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAEDV-------AFAPPLAEvlhr 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  80 ---YLSGAELLIHNAAFDVGFLNAEFAR-YQIPaleeIAAKITDTLALARAKFPGQRN-SLDALCDRLGVSNEHRvlHGA 154
Cdd:PRK07740 135 fyaFIGAGVLVAHHAGHDKAFLRHALWRtYRQP----FTHRLIDTMFLTKLLAHERDFpTLDDALAYYGIPIPRR--HHA 208

                        170
                 ....*....|.
gi 881048170 155 LLDAELLADVW 165
Cdd:PRK07740 209 LGDALMTAKLW 219
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
5-164 2.01e-14

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 71.87  E-value: 2.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   5 VLDTETTGMDAHqGDRIIEIGCIELVNREPTGNNLHLyFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGA 84
Cdd:PRK07883  19 VVDLETTGGSPA-GDAITEIGAVKVRGGEVLGEFATL-VNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  85 ELLIHNAAFDVGFLNAEFARYQIPALeeiAAKITDTLALARAKFPGQ---RNSLDALCDRLGVSNEHRvlHGALLDAELL 161
Cdd:PRK07883  97 VLVAHNAPFDIGFLRAAAARCGYPWP---GPPVLCTVRLARRVLPRDeapNVRLSTLARLFGATTTPT--HRALDDARAT 171


                 ...
gi 881048170 162 ADV 164
Cdd:PRK07883 172 VDV 174
PRK06807 PRK06807
3'-5' exonuclease;
4-151 1.69e-13

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 68.30  E-value: 1.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQgDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSG 83
Cdd:PRK06807  11 VVIDFETTGFNPYN-DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  84 AELLIHNAAFDVGFLNAEFARYQIPaleEIAAKITDTLALARAKFPGQRN-SLDALCDRLGVS-NEHRVL 151
Cdd:PRK06807  89 NVIVAHNASFDMRFLKSNVNMLGLP---EPKNKVIDTVFLAKKYMKHAPNhKLETLKRMLGIRlSSHNAF 155
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 2-168 1.89e-13

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 67.14  E-value: 1.89e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   2 RQIVLDTETTGMDAHQgDRIIEIGCIELVnrepTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYL 81
Cdd:PRK06309   3 ALIFYDTETTGTQIDK-DRIIEIAAYNGV----TSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFC 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  82 SGAELLI--HNAAFDVGFLNAEFARYQipaLEEIAAKITDTLALARAKFPG-QRNSLDALCDRLGVS--NEHRvlhgALL 156
Cdd:PRK06309  78 GTDNILVahNNDAFDFPLLRKECRRHG---LEPPTLRTIDSLKWAQKYRPDlPKHNLQYLRQVYGFEenQAHR----ALD 150

                        170
                 ....*....|..
gi 881048170 157 DAELLADVWLAM 168
Cdd:PRK06309 151 DVITLHRVFSAL 162
PRK09145 PRK09145
3'-5' exonuclease;
4-173 1.87e-11

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 61.07  E-value: 1.87e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQgDRIIEIGCIELV-NREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLS 82
Cdd:PRK09145  32 VALDCETTGLDPRR-AEIVSIAAVKIRgNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQLLAFIG 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  83 GAELLIHNAAFDVGFLNAEFARY---QIP-ALEEIAAKITDTLalaRAKFPG--QRNSLDALCDRLGVSNEHRvlHGALL 156
Cdd:PRK09145 111 NRPLVGYYLEFDVAMLNRYVRPLlgiPLPnPLIEVSALYYDKK---ERHLPDayIDLRFDAILKHLDLPVLGR--HDALN 185

                        170
                 ....*....|....*..
gi 881048170 157 DAELLADVWLAMTREQF 173
Cdd:PRK09145 186 DAIMAALIFLRLRKGDA 202
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 4-160 5.11e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 60.61  E-value: 5.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQgDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSG 83
Cdd:PRK06310  10 VCLDCETTGLDVKK-DRIIEFAAIRFTFDEVI-DSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKE 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 881048170  84 AELLI-HNAAFDVGFLNAEFARYQIPALEEiAAKITDTLALARAKFPGQRNSLDALCDRLGVsnEHRVLHGALLDAEL 160
Cdd:PRK06310  88 GDYIVgHSVGFDLQVLSQESERIGETFLSK-HYYIIDTLRLAKEYGDSPNNSLEALAVHFNV--PYDGNHRAMKDVEI 162
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 4-171 1.12e-10

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 59.60  E-value: 1.12e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQgDRIIEiGCIELVNREPTGNNLH-LYFNPERESDPGALAVHGLTTEflsqfntfdqHAQ------- 75
Cdd:PRK07942   9 AAFDLETTGVDPET-ARIVT-AALVVVDADGEVVESReWLADPGVEIPEEASAVHGITTE----------YARahgrpaa 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  76 ----EIADYL-----SGAELLIHNAAFDVGFLNAEFARYQIPALEeiAAKITDTLALARAKFP---GQRNsLDALCDRLG 143
Cdd:PRK07942  77 evlaEIADALreawaRGVPVVVFNAPYDLTVLDRELRRHGLPSLV--PGPVIDPYVIDKAVDRyrkGKRT-LTALCEHYG 153

                        170       180
                 ....*....|....*....|....*...
gi 881048170 144 VSNEHRvlHGALLDAELLADVWLAMTRE 171
Cdd:PRK07942 154 VRLDNA--HEATADALAAARVAWALARR 179
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 51-171 1.07e-09

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 57.48  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  51 PGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGAELLIHNAAFDVGFLNAEFARYQI--PALEEIAakitdTLALARAKF 128
Cdd:PRK06195  48 PINIGIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIpmPSFEYIC-----TMKLAKNFY 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 881048170 129 PGQRNS-LDALCDRLGVSNEHrvlHGALLDAELLADVWLAMTRE 171
Cdd:PRK06195 123 SNIDNArLNTVNNFLGYEFKH---HDALADAMACSNILLNISKE 163
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 5-164 1.24e-07

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 50.49  E-value: 1.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   5 VLDTETTGMdahQGDrIIEIGCIELVNREPTGNNLHLyFNPERESDPGALAVHGLTTEFLSQFNTFdqhAQEIADYLSGA 84
Cdd:PRK07983   4 VIDTETCGL---QGG-IVEIASVDVIDGKIVNPMSHL-VRPDRPISPQAMAIHRITEAMVADKPWI---EDVIPHYYGSE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  85 ELLIHNAAFDvgflnaefaRYQIPaleEIAAKITDTLALARAKFPGQRNSLDALCDRLGVSNE-------HRVLHGALLD 157
Cdd:PRK07983  76 WYVAHNASFD---------RRVLP---EMPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQtppglhhHRALYDCYIT 143


                 ....*..
gi 881048170 158 AELLADV 164
Cdd:PRK07983 144 AALLIDI 150
PRK05601 PRK05601
DNA polymerase III subunit epsilon; Validated
 20-109 1.83e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235529 [Multi-domain]  Cd Length: 377  Bit Score: 50.98  E-value: 1.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  20 RIIEIGCIELVNREPTGNNLHLYFNPEreSDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGAELLIHNAAFDVGFLN 99
Cdd:PRK05601  64 RLITIDAVTLTADGEEVEHFHAVLNPG--EDPGPFHLHGLSAEEFAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIV 141

                         90
                 ....*....|
gi 881048170 100 AEFARYQIPA 109
Cdd:PRK05601 142 SEAKRAMNAA 151
PRK08517 PRK08517
3'-5' exonuclease;
5-161 4.76e-07

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 49.25  E-value: 4.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   5 VLDTETTGmDAHQGDRIIEIGCIELVNREPTGNNLHLYFNPEreSDPGALAVHGLTTE----------FLSQFNTFDQHA 74
Cdd:PRK08517  72 FVDIETNG-SKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKE--VPEYITELTGITYEdlenapslkeVLEEFRLFLGDS 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  75 QEIAdylsgaelliHNAAFDVGFLNAEFARYqipALEEIAAKITDTLALARAKFPGQRNSLDALCDRLGVSNE--HRVLH 152
Cdd:PRK08517 149 VFVA----------HNVNFDYNFISRSLEEI---GLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEvhHRAYA 215


                 ....*....
gi 881048170 153 GALLDAELL 161
Cdd:PRK08517 216 DALAAYEIF 224
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 4-126 5.38e-07

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 48.10  E-value: 5.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHQGDRIIEIgCIELVNREPTGNN-------------LHLYFNPERESDPGALAVHGLTTEFLSQFNTF 70
Cdd:cd06136    2 VFLDLETTGLPKHNRPEITEL-CLVAVHRDHLLNTsrdkpalprvldkLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 881048170  71 D-QHAQEIADYLSGAE----LLIHNA-AFDVGFLNAEFARYQIPALEEIAAkiTDTLALARA 126
Cdd:cd06136   81 DsDTANLIKLFLRRQPkpicLVAHNGnRFDFPILRSELERLGTKLPDDILC--VDSLPAFRE 140
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 4-163 7.02e-07

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: 48.06  E-value: 7.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDaHQGDRIIEIGCIELVNREP----TGNNLHLYFNPERES--DPGALAVHGLT-----------TEFLSQ 66
Cdd:cd06134    8 VVVDVETGGFN-PQTDALLEIAAVTLEMDEQgnlyPDETFHFHILPFEGAnlDPAALEFNGIDpfhpfrfavdeKEALKE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  67 FNTFDQHAQEIADyLSGAELLIHNAAFDVGFLNAEFARYQIPALEEIAAKITDTLALARAKFpGQrNSLDALCDRLGVSN 146
Cdd:cd06134   87 IFKPIRKALKAQG-CTRAILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAY-GQ-TVLAKACQAAGIEF 163

                        170
                 ....*....|....*..
gi 881048170 147 EHRVLHGALLDAELLAD 163
Cdd:cd06134  164 DNKEAHSALYDTQKTAE 180
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 4-100 9.77e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 48.43  E-value: 9.77e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDaHQGDRIIEIGCIeLVNREPTGN------NLHLYFNPERESDPGALAVHGLTTEFLsQFNTFDQHAqeI 77
Cdd:PRK09182  40 VILDTETTGLD-PRKDEIIEIGMV-AFEYDDDGRigdvldTFGGLQQPSRPIPPEITRLTGITDEMV-AGQTIDPAA--V 114

                         90       100
                 ....*....|....*....|....
gi 881048170  78 ADYLSGAELLI-HNAAFDVGFLNA 100
Cdd:PRK09182 115 DALIAPADLIIaHNAGFDRPFLER 138
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 5-166 7.03e-04

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 40.44  E-value: 7.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   5 VLDTETTGmdAHQGDRIIEIGCIELVNREPTgNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGA 84
Cdd:PRK07246  11 VVDLEATG--AGPNASIIQVGIVIIEGGEII-DSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170  85 ELLIHNAAFDVGFLnAE---FARYqipaleEIAAKITDTLALARAKFPG-QRNSLDALCDRLGVSNEHRvlHGALLDAEL 160
Cdd:PRK07246  88 IFVAHNVKFDANLL-AEalfLEGY------ELRTPRVDTVELAQVFFPTlEKYSLSHLSRELNIDLADA--HTAIADARA 158


                 ....*.
gi 881048170 161 LADVWL 166
Cdd:PRK07246 159 TAELFL 164
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 6-142 2.25e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 37.98  E-value: 2.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   6 LDTETTGMDAHQgDRIIEIGCIEL-VNREPTGNNLHLYFNPERESDPGALAVHGLTTEFLSQFNTFDQHAQEIADYLSGA 84
Cdd:PRK09146  52 LDFETTGLDAEQ-DAIVSIGLVPFtLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEALAGK 130

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 881048170  85 ELLIHNAAFDVGFLNAefaryqipAL-----EEIAAKITDTLALARAKfpgQRNSLDALCDRL 142
Cdd:PRK09146 131 VVVVHYRRIERDFLDQ--------ALrnrigEGIEFPVIDTMEIEARI---QRKQAGGLWNRL 182
Orn cd06135
DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease ...
 6-27 4.32e-03

DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. 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. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.


Pssm-ID: 99838 [Multi-domain]  Cd Length: 173  Bit Score: 36.76  E-value: 4.32e-03
                         10        20
                 ....*....|....*....|..
gi 881048170   6 LDTETTGMDAHQgDRIIEIGCI 27
Cdd:cd06135    4 IDLEMTGLDPEK-DRILEIACI 24
YprB COG3359
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ...
 4-108 6.36e-03

Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only];


Pssm-ID: 442587 [Multi-domain]  Cd Length: 198  Bit Score: 36.46  E-value: 6.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 881048170   4 IVLDTETTGMDAHqGDRIIEIGCIELVNREPTgnnLHLYFNPERESDPGALavhgltteflsqfntfdqhaQEIADYLSG 83
Cdd:COG3359   18 LFFDIETTGLSGG-GTVIFLIGLADGEGDGFV---VRQYFGEDPGEEAALL--------------------EAFLEWLAD 73

                         90       100
                 ....*....|....*....|....*..
gi 881048170  84 AELLIH-N-AAFDVGFLNAEFARYQIP 108
Cdd:COG3359   74 YKLLVTyNgKSFDLPFLKTRFTLHRLP 100
 
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