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Conserved domains on  [gi|1816659715|ref|WP_163602189|]
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3'-5' exonuclease [Fructilactobacillus sanfranciscensis]

Protein Classification

3'-5' exonuclease( domain architecture ID 10150019)

3'-5' exonuclease similar to DNA polymerase III subunit epsilon, which is a proofreading 3'-5' exonuclease and contains the editing function of the multichain enzyme responsible for most of the replicative synthesis in bacteria

CATH:  3.30.420.10
EC:  3.1.-.-
Gene Ontology:  GO:0008408|GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 3-160 1.26e-81

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: 238.18  E-value: 1.26e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKrNRL 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG-GSL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816659715  83 VIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLeHHHNALDDSLACANILIH 160
Cdd:cd06130    80 VVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILLA 156
 
Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 3-160 1.26e-81

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: 238.18  E-value: 1.26e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKrNRL 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG-GSL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816659715  83 VIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLeHHHNALDDSLACANILIH 160
Cdd:cd06130    80 VVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILLA 156
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-159 7.14e-59

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 185.75  E-value: 7.14e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   1 MNFVAIDFETAASQRASACSVALTVVRDDQVVNEFYSLINP-ETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKR 79
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPkEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  80 NrLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHnALDDSLACANILI 159
Cdd:PRK06195   81 N-LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHD-ALADAMACSNILL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-160 1.01e-51

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 162.66  E-value: 1.01e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   2 NFVAIDFETA--ASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKr 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  80 NRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANILI 159
Cdd:COG0847    80 GAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFL 159


                  .
gi 1816659715 160 H 160
Cdd:COG0847   160 A 160
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-160 2.99e-26

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 98.14  E-value: 2.99e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715    3 FVAIDFETA--ASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRN 80
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   81 RLVIAHNNRFDNSVLRKSIERYRLPMPH-YQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLE-HHHNALDDSLACANIL 158
Cdd:smart00479  82 ILVAGNSAHFDLRFLKLEHPRLGIKQPPkLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARATAKLF 161


                   ..
gi 1816659715  159 IH 160
Cdd:smart00479 162 KK 163
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 3-159 1.09e-19

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


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 85.24  E-value: 1.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASA--CSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTF----PEIWEIIKpf 76
Cdd:TIGR01407   2 YAVVDLETTGTQLSFDkiIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFsqvaQEIYDLLE-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  77 fkrNRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACAN 156
Cdd:TIGR01407  80 ---DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAE 156


                  ...
gi 1816659715 157 ILI 159
Cdd:TIGR01407 157 LLL 159
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-158 1.30e-16

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: 72.77  E-value: 1.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   4 VAIDFETAA--SQRASACSVA--LTVVRDDQVVNEFYSLINPETD--FNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFF 77
Cdd:pfam00929   1 VVIDLETTGldPEKDEIIEIAavVIDGGENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  78 KRNRLVIAHNNRFDNSVLRKSIERY-RLPMPHY-QTLDTVKTTRKFYPNFENHKLNTVSVNLGID-LEHHHNALDDSLAC 154
Cdd:pfam00929  81 RKGNLLVAHNASFDVGFLRYDDKRFlKKPMPKLnPVIDTLILDKATYKELPGRSLDALAEKLGLEhIGRAHRALDDARAT 160


                  ....
gi 1816659715 155 ANIL 158
Cdd:pfam00929 161 AKLF 164
 
Name Accession Description Interval E-value
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 3-160 1.26e-81

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: 238.18  E-value: 1.26e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKrNRL 82
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLG-GSL 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816659715  83 VIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLeHHHNALDDSLACANILIH 160
Cdd:cd06130    80 VVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIEL-NHHDALEDARACAEILLA 156
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-159 7.14e-59

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 185.75  E-value: 7.14e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   1 MNFVAIDFETAASQRASACSVALTVVRDDQVVNEFYSLINP-ETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKR 79
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPkEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  80 NrLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHnALDDSLACANILI 159
Cdd:PRK06195   81 N-LVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHD-ALADAMACSNILL 158
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-160 1.01e-51

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 162.66  E-value: 1.01e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   2 NFVAIDFETA--ASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKr 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLG- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  80 NRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANILI 159
Cdd:COG0847    80 GAVLVAHNAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFL 159


                  .
gi 1816659715 160 H 160
Cdd:COG0847   160 A 160
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-160 2.69e-38

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 129.11  E-value: 2.69e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   1 MNFVAIDFET--AASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFK 78
Cdd:COG2176     8 LTYVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLG 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  79 rNRLVIAHNNRFDNSVLRKSIERYRLPMPHyQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANIL 158
Cdd:COG2176    88 -DAVLVAHNASFDLGFLNAALKRLGLPFDN-PVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATAELF 165


                  ..
gi 1816659715 159 IH 160
Cdd:COG2176   166 LK 167
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 4-159 6.88e-36

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: 122.41  E-value: 6.88e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   4 VAIDFET--AASQRASACSVALTVVRDD-QVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKrN 80
Cdd:cd06127     1 VVFDTETtgLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLG-G 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  81 RLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVN-LGIDLEHHHNALDDSLACANILI 159
Cdd:cd06127    80 RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAErYGIPLEGAHRALADALATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-160 2.99e-26

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 98.14  E-value: 2.99e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715    3 FVAIDFETA--ASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRN 80
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   81 RLVIAHNNRFDNSVLRKSIERYRLPMPH-YQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLE-HHHNALDDSLACANIL 158
Cdd:smart00479  82 ILVAGNSAHFDLRFLKLEHPRLGIKQPPkLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIqRAHRALDDARATAKLF 161


                   ..
gi 1816659715  159 IH 160
Cdd:smart00479 162 KK 163
polC PRK00448
DNA polymerase III PolC; Validated
 24-160 2.08e-23

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 96.06  E-value: 2.08e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   24 TVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKrNRLVIAHNNRFDNSVLRKSIERYR 103
Cdd:PRK00448   444 VKIKNGEIIDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCG-DSILVAHNASFDVGFINTNYEKLG 522

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1816659715  104 LPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANILIH 160
Cdd:PRK00448   523 LEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIK 579
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 3-160 2.25e-23

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 95.79  E-value: 2.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFET---AASQRASACSVALTVVRDDQVVNEFYSLINPEtdfnwRNI-----QVHEIHSEDVADAPTFPEIWEIIK 74
Cdd:PRK08074    5 FVVVDLETtgnSPKKGDKIIQIAAVVVEDGEILERFSSFVNPE-----RPIppfitELTGISEEMVKQAPLFEDVAPEIV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  75 PFFKrNRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLAC 154
Cdd:PRK08074   80 ELLE-GAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVT 158


                  ....*.
gi 1816659715 155 ANILIH 160
Cdd:PRK08074  159 AELFLQ 164
PRK06807 PRK06807
3'-5' exonuclease;
2-157 3.48e-23

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 93.34  E-value: 3.48e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   2 NFVAIDFETAASQ--RASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKR 79
Cdd:PRK06807    9 DYVVIDFETTGFNpyNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1816659715  80 NRLViAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEhHHNALDDSLACANI 157
Cdd:PRK06807   89 NVIV-AHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLS-SHNAFDDCITCAAV 164
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 3-159 1.09e-19

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


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 85.24  E-value: 1.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASA--CSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTF----PEIWEIIKpf 76
Cdd:TIGR01407   2 YAVVDLETTGTQLSFDkiIQIGIVVVEDGEIVDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFsqvaQEIYDLLE-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  77 fkrNRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACAN 156
Cdd:TIGR01407  80 ---DGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAE 156


                  ...
gi 1816659715 157 ILI 159
Cdd:TIGR01407 157 LLL 159
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 29-150 4.44e-18

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 78.31  E-value: 4.44e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  29 DQVVNE-FYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRNRLVIAHNN-RFDNSVLRKSIERYRLPM 106
Cdd:PRK06309   28 NGVTSEsFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDNILVAHNNdAFDFPLLRKECRRHGLEP 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1816659715 107 PHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDD 150
Cdd:PRK06309  108 PTLRTIDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDD 151
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 3-160 1.20e-17

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 79.35  E-value: 1.20e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFE-TAASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPE----IWEIIKpff 77
Cdd:PRK07246    9 YAVVDLEaTGAGPNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQvarhIYDLIE--- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  78 krNRLVIAHNNRFDNSVLRKSI--ERYRLPMPHyqtLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACA 155
Cdd:PRK07246   86 --DCIFVAHNVKFDANLLAEALflEGYELRTPR---VDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADARATA 160


                  ....*
gi 1816659715 156 NILIH 160
Cdd:PRK07246  161 ELFLK 165
PRK06063 PRK06063
DEDDh family exonuclease;
3-158 1.37e-17

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 78.20  E-value: 1.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETA--ASQRASACSVALTVVRDD-QVVNEFYSLINPETDFNwrNIQVHEIHSEDVADAPTFPEIWEIIKPFFkR 79
Cdd:PRK06063   17 WAVVDVETSgfRPGQARIISLAVLGLDADgNVEQSVVTLLNPGVDPG--PTHVHGLTAEMLEGQPQFADIAGEVAELL-R 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1816659715  80 NRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANIL 158
Cdd:PRK06063   94 GRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVLAGIL 172
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 4-158 1.30e-16

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: 72.77  E-value: 1.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   4 VAIDFETAA--SQRASACSVA--LTVVRDDQVVNEFYSLINPETD--FNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFF 77
Cdd:pfam00929   1 VVIDLETTGldPEKDEIIEIAavVIDGGENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  78 KRNRLVIAHNNRFDNSVLRKSIERY-RLPMPHY-QTLDTVKTTRKFYPNFENHKLNTVSVNLGID-LEHHHNALDDSLAC 154
Cdd:pfam00929  81 RKGNLLVAHNASFDVGFLRYDDKRFlKKPMPKLnPVIDTLILDKATYKELPGRSLDALAEKLGLEhIGRAHRALDDARAT 160


                  ....
gi 1816659715 155 ANIL 158
Cdd:pfam00929 161 AKLF 164
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
3-158 4.79e-16

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 74.57  E-value: 4.79e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASqraSACSVALT----V-VRDDQVVNEFYSLINPEtdfnwRNI-----QVHEIHSEDVADAPTfpeIWEI 72
Cdd:PRK07883   17 FVVVDLETTGG---SPAGDAITeigaVkVRGGEVLGEFATLVNPG-----RPIppfitVLTGITTAMVAGAPP---IEEV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  73 IKPF--FKRNRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNFE--NHKLNTVSVNLGIDLEHHHNAL 148
Cdd:PRK07883   86 LPAFleFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEapNVRLSTLARLFGATTTPTHRAL 165

                         170
                  ....*....|
gi 1816659715 149 DDSLACANIL 158
Cdd:PRK07883  166 DDARATVDVL 175
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 3-165 3.05e-15

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 71.01  E-value: 3.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAA--SQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRN 80
Cdd:PRK06310    9 FVCLDCETTGldVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKEG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  81 RLVIAHNNRFDNSVLRKSIERYRLP--MPHYQTLDTVKTTRKfYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANIL 158
Cdd:PRK06310   89 DYIVGHSVGFDLQVLSQESERIGETflSKHYYIIDTLRLAKE-YGDSPNNSLEALAVHFNVPYDGNHRAMKDVEINIKVF 167


                  ....*..
gi 1816659715 159 IHEHQQF 165
Cdd:PRK06310  168 KHLCKRF 174
PRK08517 PRK08517
3'-5' exonuclease;
2-158 1.61e-12

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 63.50  E-value: 1.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   2 NFVAIDFETAAS--QRASACSVALTVVRDDQVVNEFYSLInpETDFNWRNI-QVHEIHSEDVADAPTFPEIWEIIKPFFK 78
Cdd:PRK08517   69 VFCFVDIETNGSkpKKHQIIEIGAVKVKNGEIIDRFESFV--KAKEVPEYItELTGITYEDLENAPSLKEVLEEFRLFLG 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  79 rNRLVIAHNNRFDNSVLRKSIERYRLPMPHYQTLDTVKTTRKFYPNfENHKLNTVSVNLGIDLEHHHNALDDSLACANIL 158
Cdd:PRK08517  147 -DSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIES-PRYGLSFLKELLGIEIEVHHRAYADALAAYEIF 224
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 33-151 9.33e-12

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: 59.85  E-value: 9.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  33 NEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRNRLVIaHNNRFDNSVLRKSIERYRLP---MPHY 109
Cdd:cd06131    35 NTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRGAELVI-HNASFDVGFLNAELSLLGLGkkiIDFC 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1816659715 110 QTLDTVKTTRKFYPNFENhKLNTVSVNLGIDLEHH--HNALDDS 151
Cdd:cd06131   114 RVIDTLALARKKFPGKPN-SLDALCKRFGIDNSHRtlHGALLDA 156
Rv2179c-like pfam16473
3'-5' exoribonuclease Rv2179c-like domain; This is a highly divergent 3' exoribonuclease ...
 2-158 8.85e-11

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


Pssm-ID: 406788  Cd Length: 177  Bit Score: 57.82  E-value: 8.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   2 NFVAIDFETAAS-QRASACSVALTVVR--DDQVVNEFYSLINPETD------FNWRNIQVHEIHSEDVA------DAPTF 66
Cdd:pfam16473   1 NHLMIDIETLGNePTAPIVSIGAVFFDpeTGELGKEFYARIDLESSmsagatIDADTILWWLKQSSEARaqllgdDAPSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  67 PEIWEIIKPFFKRNRL-----VIAHNNRFDNSVLRKSIERYRLPMP--HYQTLDtVKTTRKFYPnfenhklntvsvNLGI 139
Cdd:pfam16473  81 PDALLDLNDFIRDNGDpkslkVWGNGASFDNVILRAAFERGGLPAPwkYWNDRD-VRTIVALGP------------ELGY 147

                         170       180
                  ....*....|....*....|....*.
gi 1816659715 140 DLEH-------HHNALDDSLACANIL 158
Cdd:pfam16473 148 DPKRdipfegvKHNALDDAIHQAKYV 173
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 6-160 2.88e-10

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 57.04  E-value: 2.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   6 IDFETAASQrASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTfpeIWEIIkPFFKRNRLVIA 85
Cdd:PRK07983    5 IDTETCGLQ-GGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPW---IEDVI-PHYYGSEWYVA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  86 HNNRFDNSVlrksieryrLPMPHYQTLDTVKTTRKFYPN--------FENHKLNtVSVNLGIdleHHHNALDDSLACANI 157
Cdd:PRK07983   80 HNASFDRRV---------LPEMPGEWICTMKLARRLWPGikysnmalYKSRKLN-VQTPPGL---HHHRALYDCYITAAL 146


                  ...
gi 1816659715 158 LIH 160
Cdd:PRK07983  147 LID 149
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-160 3.14e-10

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 56.02  E-value: 3.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   1 MNFVAIDFE--TAASQRASACSV------ALTVVRDDQVVNEFYSLINPEtdfnwRNIQVHE-------IHSEDVADAPT 65
Cdd:COG5018     2 MKYLVIDLEatCWDGKPPPGFPMeiieigAVKVDENGEIIDEFSSFVKPV-----RRPKLSPfcteltgITQEDVDSAPS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  66 FPEIWEIIKPFFKRNRLVIAHNNRFDNSVLRKSIERYRLPMP-HYQTLDtVKttrKFYPNFENHKlNTVSVN-----LGI 139
Cdd:COG5018    77 FAEAIEDFKKWIGSEDYILCSWGDYDRKQLERNCRFHGVPYPfGDRHIN-LK---KLFALYFGLK-KRIGLKkalelLGL 151

                         170       180
                  ....*....|....*....|..
gi 1816659715 140 DLE-HHHNALDDSLACANILIH 160
Cdd:COG5018   152 EFEgTHHRALDDARNTAKLFKK 173
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 22-158 7.72e-10

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: 55.53  E-value: 7.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  22 ALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPeiwEIIKPFFK--RNRLVIAHNNRFDNSVLRKSI 99
Cdd:TIGR00573  30 AVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFK---EIAEDFADyiRGAELVIHNASFDVGFLNYEF 106

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715 100 ERYRLPMPHYQTL-DTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACANIL 158
Cdd:TIGR00573 107 SKLYKVEPKTNDViDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFIL 166
PRK07740 PRK07740
hypothetical protein; Provisional
 3-160 3.20e-09

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 54.29  E-value: 3.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAA---SQRASACSVALTVVRDDQVVNE-FYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFK 78
Cdd:PRK07740   61 FVVFDLETTGfspQQGDEILSIGAVKTKGGEVETDtFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAFIG 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  79 RNRLV---IAHNNRFDNSVLRKSierYRLPMPHyQTLDTVKTTRKFYPNFENHKLNTVSVNLGIDLEHHHNALDDSLACA 155
Cdd:PRK07740  141 AGVLVahhAGHDKAFLRHALWRT---YRQPFTH-RLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMTA 216


                  ....*
gi 1816659715 156 NILIH 160
Cdd:PRK07740  217 KLWAI 221
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 3-160 1.18e-07

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: 49.14  E-value: 1.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETAASQRASAC---------SVALTVVRDDQVVNEFYSLINPEtdfnwRNIQVHE-------IHSEDVADAPTF 66
Cdd:cd06133     1 YLVIDFEATCWEGNSKPdypneiieiGAVLVDVKTKEIIDTFSSYVKPV-----INPKLSDfcteltgITQEDVDNAPSF 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  67 PEIWEIIKPFF-KRNRLVIAHNNRFDNSVLRKSIERY---RLPMPHYQTLDTvkttRKFYPNFENHKLNTVSVN----LG 138
Cdd:cd06133    76 PEVLKEFLEWLgKNGKYAFVTWGDWDLKDLLQNQCKYkiiNLPPFFRQWIDL----KKEFAKFYGLKKRTGLSKaleyLG 151

                         170       180
                  ....*....|....*....|...
gi 1816659715 139 IDLE-HHHNALDDSLACANILIH 160
Cdd:cd06133   152 LEFEgRHHRGLDDARNIARILKR 174
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 33-151 2.34e-05

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 43.31  E-value: 2.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  33 NEFYSLINPETDFNWRNIQVHEIHSEDVADAPTFPEIWEIIKPFFKRNRLVIaHNNRFD----NSVLRKsIERYRLPMPH 108
Cdd:PRK05711   40 RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAELII-HNAPFDigfmDYEFAL-LGRDIPKTNT 117

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1816659715 109 Y-QTLDTVKTTRKFYPNFENhKLNTVSVNLGIDLEHH--HNALDDS 151
Cdd:PRK05711  118 FcKVTDTLAMARRMFPGKRN-SLDALCKRYGIDNSHRtlHGALLDA 162
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 4-157 4.44e-04

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 39.57  E-value: 4.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   4 VAIDFET--AASQRASACSVALTVVRDDQVVNEFYS-LINPETDFNWRNIQVHEIHSEDVAD-----APTFPEIWEIIKP 75
Cdd:PRK07942    9 AAFDLETtgVDPETARIVTAALVVVDADGEVVESREwLADPGVEIPEEASAVHGITTEYARAhgrpaAEVLAEIADALRE 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  76 FFKRNRLVIAHNNRFDNSVLRKSIERYRL----PMPHYQ--TLDTVKTT-RKfypnfENHKLNTVSVNLGIDLEHHHNAL 148
Cdd:PRK07942   89 AWARGVPVVVFNAPYDLTVLDRELRRHGLpslvPGPVIDpyVIDKAVDRyRK-----GKRTLTALCEHYGVRLDNAHEAT 163


                  ....*....
gi 1816659715 149 DDSLACANI 157
Cdd:PRK07942  164 ADALAAARV 172
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 3-161 7.89e-04

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: 38.47  E-value: 7.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   3 FVAIDFETA----------------ASQRASACSVALTVVRDDQVVNEFYSLINPETDFNWRNIQVHEIHSEDVADAPTF 66
Cdd:cd06136     1 FVFLDLETTglpkhnrpeitelclvAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  67 PE-IWEIIKPFFKRNRLVI---AHN-NRFDNSVLRKSIERYRLPMPH-YQTLDTVKTTRKFYPNFEnhklNTVSVNLGID 140
Cdd:cd06136    81 DSdTANLIKLFLRRQPKPIclvAHNgNRFDFPILRSELERLGTKLPDdILCVDSLPAFRELDQSLG----SLYKRLFGQE 156

                         170       180
                  ....*....|....*....|.
gi 1816659715 141 LEHHHNALDDSLACANILIHE 161
Cdd:cd06136   157 PKNSHTAEGDVLALLKCALHK 177
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 4-153 7.56e-03

DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins; This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T.


Pssm-ID: 99847  Cd Length: 152  Bit Score: 35.18  E-value: 7.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715   4 VAIDFE---TAASQRASAC-SVALTVVRDDQVVNEFYSLINPETDFNWRniqVHEIHSEDVADAPTFPEIWEIIKPFFKr 79
Cdd:cd06144     1 VALDCEmvgVGPDGSESALaRVSIVNEDGNVVYDTYVKPQEPVTDYRTA---VSGIRPEHLKDAPDFEEVQKKVAELLK- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1816659715  80 NRLVIAHNNRFDNSVLrksieryRLPMPHYQTLDTVKttrkfYPNFENH-KLNTVSVN------LGIDL-EHHHNALDDS 151
Cdd:cd06144    77 GRILVGHALKNDLKVL-------KLDHPKKLIRDTSK-----YKPLRKTaKGKSPSLKklakqlLGLDIqEGEHSSVEDA 144


                  ..
gi 1816659715 152 LA 153
Cdd:cd06144   145 RA 146
 
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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