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Conserved domains on  [gi|2789488076|ref|WP_370807741|]
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exonuclease domain-containing protein [Faecalibacillus intestinalis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
polC super family cl35100
DNA polymerase III PolC; Validated
 5-230 1.55e-90

DNA polymerase III PolC; Validated


The actual alignment was detected with superfamily member PRK00448:

Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 290.97  E-value: 1.55e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076    5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYR 84
Cdd:PRK00448   469 TTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHR 548

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   85 LGNVCRVYRVNYDDDvaHRADYDAEVLGAVFTTMLHSIMQSGNYNLLDLNK-LQKDDAYKIVFPYHMTALALNKEGLKNM 163
Cdd:PRK00448   549 LNTLAKKFGVELEHH--HRADYDAEATAYLLIKFLKDLKEKGITNLDELNKkLGSEDAYKKARPKHATILVKNQVGLKNL 626

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2789488076  164 FKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALNSSDEKLEQLLEFYDYVEIQP 230
Cdd:PRK00448   627 FKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQP 693
 
Name Accession Description Interval E-value
polC PRK00448
DNA polymerase III PolC; Validated
 5-230 1.55e-90

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 290.97  E-value: 1.55e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076    5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYR 84
Cdd:PRK00448   469 TTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHR 548

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   85 LGNVCRVYRVNYDDDvaHRADYDAEVLGAVFTTMLHSIMQSGNYNLLDLNK-LQKDDAYKIVFPYHMTALALNKEGLKNM 163
Cdd:PRK00448   549 LNTLAKKFGVELEHH--HRADYDAEATAYLLIKFLKDLKEKGITNLDELNKkLGSEDAYKKARPKHATILVKNQVGLKNL 626

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2789488076  164 FKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALNSSDEKLEQLLEFYDYVEIQP 230
Cdd:PRK00448   627 FKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQP 693
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 4-130 1.45e-46

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 152.61  E-value: 1.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNqKPITNPVIDSLALARAIMKPMKSY 83
Cdd:COG2176    57 FITELTGITDEMVADAPPFEEVLPEFLEFLGDAVLVAHNASFDLGFLNAALKRLG-LPFDNPVLDTLELARRLLPELKSY 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2789488076  84 RLGNVCRVYRVNYDDdvAHRADYDAEVLGAVFTTMLHSIMQSGNYNL 130
Cdd:COG2176   136 KLDTLAERLGIPLED--RHRALGDAEATAELFLKLLEKLEEKGITTL 180
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-115 5.72e-38

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: 129.73  E-value: 5.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSY 83
Cdd:cd06127    48 EATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSH 127

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2789488076  84 RLGNVCRvYRVNYDDDVAHRADYDAEVLGAVF 115
Cdd:cd06127   128 RLGLLLA-ERYGIPLEGAHRALADALATAELL 158
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 5-169 2.43e-28

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: 106.77  E-value: 2.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQK-PITNPVIDSLALARAI--MKPMK 81
Cdd:TIGR00573  57 AIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVePKTNDVIDTTDTLQYArpEFPGK 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  82 SYRLGNVCRVYRVNYDDDVAHRADYDAEVLGAVFTTMLHSIMQsgnYNLLDLNKLQkddaykivfPYHMTALALNKEGLK 161
Cdd:TIGR00573 137 RNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQTK---YGENEGQQSR---------PYHAIKSIVKKDMLL 204


                  ....*...
gi 2789488076 162 NMFKIVSE 169
Cdd:TIGR00573 205 KLIKAVST 212
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 4-119 5.35e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 101.99  E-value: 5.35e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076    4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHN-AKFDIGFLNESLKRLNQK-PITNPVIDSLALARAIMKPMK 81
Cdd:smart00479  49 YATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKqPPKLPVIDTLKLARATNPGLP 128

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2789488076   82 SYRLGNVCRVYRVnYDDDVAHRADYDAEVLGAVFTTML 119
Cdd:smart00479 129 KYSLKKLAKRLLL-EVIQRAHRALDDARATAKLFKKLL 165
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-115 4.31e-22

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: 88.95  E-value: 4.31e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFG-DAILVAHNAKFDIGFLNESLKRLNQK--PITNPVIDSLALARAIMKPM 80
Cdd:pfam00929  51 ECTKFTGITQAMLDNKPSFEEVLEEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKKpmPKLNPVIDTLILDKATYKEL 130

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2789488076  81 KSYRLGNVCRVYRVNYDDDvAHRADYDAEVLGAVF 115
Cdd:pfam00929 131 PGRSLDALAEKLGLEHIGR-AHRALDDARATAKLF 164
 
Name Accession Description Interval E-value
polC PRK00448
DNA polymerase III PolC; Validated
 5-230 1.55e-90

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 290.97  E-value: 1.55e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076    5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYR 84
Cdd:PRK00448   469 TTELTGITDDMVKDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHR 548

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   85 LGNVCRVYRVNYDDDvaHRADYDAEVLGAVFTTMLHSIMQSGNYNLLDLNK-LQKDDAYKIVFPYHMTALALNKEGLKNM 163
Cdd:PRK00448   549 LNTLAKKFGVELEHH--HRADYDAEATAYLLIKFLKDLKEKGITNLDELNKkLGSEDAYKKARPKHATILVKNQVGLKNL 626

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2789488076  164 FKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALNSSDEKLEQLLEFYDYVEIQP 230
Cdd:PRK00448   627 FKLVSLSNTKYFYRVPRIPRSLLDKYREGLLIGSACEEGEVFDAVLQKGDEELEEIAKFYDYIEIQP 693
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 4-130 1.45e-46

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 152.61  E-value: 1.45e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNqKPITNPVIDSLALARAIMKPMKSY 83
Cdd:COG2176    57 FITELTGITDEMVADAPPFEEVLPEFLEFLGDAVLVAHNASFDLGFLNAALKRLG-LPFDNPVLDTLELARRLLPELKSY 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2789488076  84 RLGNVCRVYRVNYDDdvAHRADYDAEVLGAVFTTMLHSIMQSGNYNL 130
Cdd:COG2176   136 KLDTLAERLGIPLED--RHRALGDAEATAELFLKLLEKLEEKGITTL 180
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 6-119 1.22e-39

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 134.15  E-value: 1.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   6 SQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYRL 85
Cdd:COG0847    51 TAIHGITDEDVADAPPFAEVLPELLEFLGGAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSL 130

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2789488076  86 GNVCRVYrvNYDDDVAHRADYDAEVLGAVFTTML 119
Cdd:COG0847   131 DALCERL--GIPFDERHRALADAEATAELFLALL 162
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-115 5.72e-38

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: 129.73  E-value: 5.72e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSY 83
Cdd:cd06127    48 EATAIHGITDEMLADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSH 127

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2789488076  84 RLGNVCRvYRVNYDDDVAHRADYDAEVLGAVF 115
Cdd:cd06127   128 RLGLLLA-ERYGIPLEGAHRALADALATAELL 158
PHP_PolIIIA_POLC cd07435
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at ...
 140-230 3.32e-37

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in different location compare to dnaE1, 2, and 3. The PHP domain has four conserved sequence motifs and and contains an invariant histidine that is involved in metal ion coordination.The PHP domain of PolC is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. PHP domains found in dnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. In contrast, PolC PHP lacks detectable nuclease activity.


Pssm-ID: 213990 [Multi-domain]  Cd Length: 268  Bit Score: 131.06  E-value: 3.32e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076 140 DAYkIVFPYHMTALALNKEGLKNMFKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALN-SSDEKLEQ 218
Cdd:cd07435    64 EAY-LVDPYHITILVKNQTGLKNLYKLVSLSHTKYFYRVPRIPKSELEKYREGLLIGSACENGELFEAALNkKSDEELEE 142

                          90
                  ....*....|..
gi 2789488076 219 LLEFYDYVEIQP 230
Cdd:cd07435   143 IASFYDYIEIQP 154
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 5-124 1.06e-29

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 116.59  E-value: 1.06e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYR 84
Cdd:PRK08074   54 ITELTGISEEMVKQAPLFEDVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYK 133

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2789488076  85 LGNVCRVYRVNYDDdvAHRADYDAEVLGAVFTTMLHSIMQ 124
Cdd:PRK08074  134 LRDLSEELGLEHDQ--PHRADSDAEVTAELFLQLLNKLER 171
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 5-169 2.43e-28

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: 106.77  E-value: 2.43e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQK-PITNPVIDSLALARAI--MKPMK 81
Cdd:TIGR00573  57 AIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVePKTNDVIDTTDTLQYArpEFPGK 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  82 SYRLGNVCRVYRVNYDDDVAHRADYDAEVLGAVFTTMLHSIMQsgnYNLLDLNKLQkddaykivfPYHMTALALNKEGLK 161
Cdd:TIGR00573 137 RNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQTK---YGENEGQQSR---------PYHAIKSIVKKDMLL 204


                  ....*...
gi 2789488076 162 NMFKIVSE 169
Cdd:TIGR00573 205 KLIKAVST 212
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 4-119 5.35e-27

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 101.99  E-value: 5.35e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076    4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHN-AKFDIGFLNESLKRLNQK-PITNPVIDSLALARAIMKPMK 81
Cdd:smart00479  49 YATEIHGITPEMLDDAPTFEEVLEELLEFLRGRILVAGNsAHFDLRFLKLEHPRLGIKqPPKLPVIDTLKLARATNPGLP 128

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2789488076   82 SYRLGNVCRVYRVnYDDDVAHRADYDAEVLGAVFTTML 119
Cdd:smart00479 129 KYSLKKLAKRLLL-EVIQRAHRALDDARATAKLFKKLL 165
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
4-109 2.14e-26

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 106.54  E-value: 2.14e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKP--MK 81
Cdd:PRK07883   64 FITVLTGITTAMVAGAPPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRdeAP 143

                          90       100       110
                  ....*....|....*....|....*....|
gi 2789488076  82 SYRLGNVCRVYRVnyddDVA--HRADYDAE 109
Cdd:PRK07883  144 NVRLSTLARLFGA----TTTptHRALDDAR 169
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 11-118 2.22e-25

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: 97.60  E-value: 2.22e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNP---VIDSLALARAiMKPMKSYRLGN 87
Cdd:cd06131    57 ITDEFLADKPKFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDfcrVIDTLALARK-KFPGKPNSLDA 135

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2789488076  88 VCRVYRVNYDDDVAHRADYDAEVLGAVFTTM 118
Cdd:cd06131   136 LCKRFGIDNSHRTLHGALLDAELLAEVYLEL 166
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 11-118 3.88e-25

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 98.78  E-value: 3.88e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQK-PITNP---VIDSLALARAiMKPMKSYRLG 86
Cdd:PRK05711   62 ITDEFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDiPKTNTfckVTDTLAMARR-MFPGKRNSLD 140

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2789488076  87 NVCRVYRVnyddDVAHR----ADYDAEVLGAVFTTM 118
Cdd:PRK05711  141 ALCKRYGI----DNSHRtlhgALLDAEILAEVYLAM 172
PRK06807 PRK06807
3'-5' exonuclease;
4-145 1.29e-24

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 99.12  E-value: 1.29e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSY 83
Cdd:PRK06807   57 RITSLTGITNYRVSDAPTIEEVLPLFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNH 136

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2789488076  84 RLGNVCRVYRVNYDddvAHRADYDAEVLGAVFTTmlHSIMQSGNYNLLDLNKLQKDDAYKIV 145
Cdd:PRK06807  137 KLETLKRMLGIRLS---SHNAFDDCITCAAVYQK--CASIEEEAKRKSNKEVLDETAVYEAV 193
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 7-109 6.76e-23

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: 90.65  E-value: 6.76e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   7 QLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYRLG 86
Cdd:cd06130    49 AIHGITPEDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLN 128

                          90       100
                  ....*....|....*....|...
gi 2789488076  87 NVCRVYRVNYDDdvaHRADYDAE 109
Cdd:cd06130   129 TVAEHLGIELNH---HDALEDAR 148
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-115 4.31e-22

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: 88.95  E-value: 4.31e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFG-DAILVAHNAKFDIGFLNESLKRLNQK--PITNPVIDSLALARAIMKPM 80
Cdd:pfam00929  51 ECTKFTGITQAMLDNKPSFEEVLEEFLEFLRkGNLLVAHNASFDVGFLRYDDKRFLKKpmPKLNPVIDTLILDKATYKEL 130

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2789488076  81 KSYRLGNVCRVYRVNYDDDvAHRADYDAEVLGAVF 115
Cdd:pfam00929 131 PGRSLDALAEKLGLEHIGR-AHRALDDARATAKLF 164
PRK08517 PRK08517
3'-5' exonuclease;
5-108 3.79e-19

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 83.15  E-value: 3.79e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKsYR 84
Cdd:PRK08517  117 ITELTGITYEDLENAPSLKEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPR-YG 195

                          90       100
                  ....*....|....*....|....
gi 2789488076  85 LGNVCRVyrVNYDDDVAHRADYDA 108
Cdd:PRK08517  196 LSFLKEL--LGIEIEVHHRAYADA 217
PRK07740 PRK07740
hypothetical protein; Provisional
 5-133 3.99e-19

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 82.79  E-value: 3.99e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   5 VSQLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYR 84
Cdd:PRK07740  111 ILELTGITAEDVAFAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPT 190

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2789488076  85 LGNVCRVYRVNYDDdvAHRADYDAEVLGAVFTTMLHSIMQSGNYNLLDL 133
Cdd:PRK07740  191 LDDALAYYGIPIPR--RHHALGDALMTAKLWAILLVEAQQRGITTLHDL 237
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 11-115 2.21e-13

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 67.16  E-value: 2.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQILEFFGDA-ILVAHNAKFDIGFLNESLKRLNQ--KPITNPVIDSLALARAIMK-PMKSyrLG 86
Cdd:PRK06310   63 ISDAMLRDKPKIAEVFPQIKGFFKEGdYIVGHSVGFDLQVLSQESERIGEtfLSKHYYIIDTLRLAKEYGDsPNNS--LE 140

                          90       100
                  ....*....|....*....|....*....
gi 2789488076  87 NVCRVYRVNYddDVAHRADYDAEVLGAVF 115
Cdd:PRK06310  141 ALAVHFNVPY--DGNHRAMKDVEINIKVF 167
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 6-132 3.88e-13

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 66.37  E-value: 3.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   6 SQLTNITNEMVADAPTIKEFLPQILEFFG-DAILVAHNA-KFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSY 83
Cdd:PRK06309   50 SKIHGITTDEVADAPKFPEAYQKFIEFCGtDNILVAHNNdAFDFPLLRKECRRHGLEPPTLRTIDSLKWAQKYRPDLPKH 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2789488076  84 RLGNVCRVYrvNYDDDVAHRADYDAEVLGAVFTTMLHSIMQSGNYNLLD 132
Cdd:PRK06309  130 NLQYLRQVY--GFEENQAHRALDDVITLHRVFSALVGDLSPQQVYDLLN 176
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 8-124 1.04e-11

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 63.94  E-value: 1.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   8 LTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLkRLNQKPITNPVIDSLALARAIMKPMKSYRLGN 87
Cdd:PRK07246   59 LTGITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEAL-FLEGYELRTPRVDTVELAQVFFPTLEKYSLSH 137

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2789488076  88 VCRVYRVNYDDdvAHRADYDAEVLGAVFTTMLHSIMQ 124
Cdd:PRK07246  138 LSRELNIDLAD--AHTAIADARATAELFLKLLQKIES 172
PHP_PolIIIA_DnaE3 cd12113
Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III ...
 148-229 3.30e-10

Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group.


Pssm-ID: 213997 [Multi-domain]  Cd Length: 283  Bit Score: 58.61  E-value: 3.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076 148 YHMTALALNKEGLKNMFKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALNSSDEKLEQLLEFYD--- 224
Cdd:cd12113    86 YHLVLLAKNEEGYRNLMKLVSLAYLEGFYYKPRIDKELLAKYSEGLIALSACLAGEIPQLLLNGDEEEAREAALEYRdif 165

                          90
                  ....*....|
gi 2789488076 225 -----YVEIQ 229
Cdd:cd12113   166 gkdnfYLELQ 175
dnaE PRK06826
DNA polymerase III DnaE; Reviewed
 138-229 1.08e-08

DNA polymerase III DnaE; Reviewed


Pssm-ID: 235868 [Multi-domain]  Cd Length: 1151  Bit Score: 54.90  E-value: 1.08e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  138 KDDAYkivfpYHMTALALNKEGLKNMFKIVSEANTTYFHDGSRIPKERLEYYRKGLLYGTSCYRSDVFEAALNSSDEKLE 217
Cdd:PRK06826    83 IDNET-----YHLVLLAKNETGYKNLMKIVSKAFTEGFYYKPRVDHELLKEHSEGLIALSACLAGEVPRYILKGNYEKAK 157

                           90       100
                   ....*....|....*....|
gi 2789488076  218 QLLEFYD--------YVEIQ 229
Cdd:PRK06826   158 EAALFYKdifgkenfYLELQ 177
PRK06063 PRK06063
DEDDh family exonuclease;
11-121 3.62e-08

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 52.78  E-value: 3.62e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYRLGNVCR 90
Cdd:PRK06063   70 LTAEMLEGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAA 149

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2789488076  91 VYRVNydDDVAHRADYDAEVLGAVFTTMLHS 121
Cdd:PRK06063  150 HWGVP--QQRPHDALDDARVLAGILRPSLER 178
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 11-123 3.94e-08

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 52.03  E-value: 3.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQileFFGDAILVAHNAKFDIGFLNEslkrlnqkpITNPVIDSLALARAIMKPMKSyrlGNVCR 90
Cdd:PRK07983   53 ITEAMVADKPWIEDVIPH---YYGSEWYVAHNASFDRRVLPE---------MPGEWICTMKLARRLWPGIKY---SNMAL 117

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2789488076  91 VYRVNYDDDV-----AHRADYDAEVLGAvfttMLHSIM 123
Cdd:PRK07983  118 YKSRKLNVQTppglhHHRALYDCYITAA----LLIDIM 151
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 36-119 4.05e-08

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: 51.52  E-value: 4.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  36 AILVAHNAKFDIGFLNESLKRLNQKpiTNP-----VIDSLALArAIMkpMKSYRLGNVCRVYRVNYDDDVAHRADYDAEV 110
Cdd:cd06134   103 AILVGHNAHFDLGFLNAAVARCKIK--RNPfhpfsTFDTATLA-GLA--YGQTVLAKACQAAGIEFDNKEAHSALYDTQK 177


                  ....*....
gi 2789488076 111 LGAVFTTML 119
Cdd:cd06134   178 TAELFCKIV 186
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 7-88 4.73e-08

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 52.48  E-value: 4.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   7 QLTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIMKPMKSYRLG 86
Cdd:PRK06195   52 GIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLN 131


                  ..
gi 2789488076  87 NV 88
Cdd:PRK06195  132 TV 133
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 11-108 8.85e-06

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 45.35  E-value: 8.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVAD-----APTIKEFLPQILEFFGDAI-LVAHNAKFDIGFLNESLKRLNQKPITN-PVIDSLALARAIMKPMKSY 83
Cdd:PRK07942   63 ITTEYARAhgrpaAEVLAEIADALREAWARGVpVVVFNAPYDLTVLDRELRRHGLPSLVPgPVIDPYVIDKAVDRYRKGK 142

                          90       100
                  ....*....|....*....|....*.
gi 2789488076  84 R-LGNVCRVYRVNYDDdvAHRADYDA 108
Cdd:PRK07942  143 RtLTALCEHYGVRLDN--AHEATADA 166
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 4-119 5.57e-05

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 42.54  E-value: 5.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFG--DAILVAhNAKFDIGFLNESLKRLNQK-PITNPVIDSLALARAIMKPM 80
Cdd:COG5018    59 FCTELTGITQEDVDSAPSFAEAIEDFKKWIGseDYILCS-WGDYDRKQLERNCRFHGVPyPFGDRHINLKKLFALYFGLK 137

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2789488076  81 KSYRLGNVCRVYRVNYDDDvAHRADYDAEVLGAVFTTML 119
Cdd:COG5018   138 KRIGLKKALELLGLEFEGT-HHRALDDARNTAKLFKKIL 175
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 11-108 5.73e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 42.99  E-value: 5.73e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076  11 ITNEMVADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVIDSLALARAIM------------- 77
Cdd:PRK09146  105 ITHSELQDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEIEARIQrkqagglwnrlkg 184

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2789488076  78 KPMKSYRLGNvCRVyRVNYDDDVAHRADYDA 108
Cdd:PRK09146  185 KKPESIRLAD-SRL-RYGLPAYSPHHALTDA 213
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 4-50 1.70e-04

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 41.88  E-value: 1.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2789488076   4 RVSQLTNITNEMVADaptiKEFLPQILE-FFGDA-ILVAHNAKFDIGFL 50
Cdd:PRK09182   92 EITRLTGITDEMVAG----QTIDPAAVDaLIAPAdLIIAHNAGFDRPFL 136
PRK09145 PRK09145
3'-5' exonuclease;
16-68 2.14e-04

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 41.04  E-value: 2.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2789488076  16 VADAPTIKEFLPQILEFFGDAILVAHNAKFDIGFLNESLKRLNQKPITNPVID 68
Cdd:PRK09145   92 LEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIE 144
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 4-119 3.87e-04

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: 39.90  E-value: 3.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2789488076   4 RVSQLTNITNEMVADAPTIKEFLPQILEFFGD---AILVAhNAKFDIGFLNESLKRLNQK---PITNPVIDSLALARAIM 77
Cdd:cd06133    57 FCTELTGITQEDVDNAPSFPEVLKEFLEWLGKngkYAFVT-WGDWDLKDLLQNQCKYKIInlpPFFRQWIDLKKEFAKFY 135

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2789488076  78 KPMKSYRLGNVCRVYRVNYDDDvAHRADYDAEVLGAVFTTML 119
Cdd:cd06133   136 GLKKRTGLSKALEYLGLEFEGR-HHRGLDDARNIARILKRLL 176
PRK07247 PRK07247
3'-5' exonuclease;
8-52 5.88e-03

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 36.68  E-value: 5.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2789488076   8 LTNITNEMVADAPTIKEFLPQILEFFGDAILVAHNA-KFDIGFLNE 52
Cdd:PRK07247   57 LTGITADKIADAPKVEEVLAAFKEFVGELPLIGYNAqKSDLPILAE 102
DnaQ_like_exo cd06125
DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; The DnaQ-like exonuclease ...
 36-75 7.88e-03

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: 34.72  E-value: 7.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2789488076  36 AILVAHNAKFDIGFLNESLKRLNQK--PITNPVIDSLALARA 75
Cdd:cd06125    45 AILVGHNGSFDLPFLNNRCAELGLKypLLAGSWIDTIKLAAD 86
 
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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