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Conserved domains on  [gi|1224246892|ref|WP_092273583|]
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exonuclease domain-containing protein [Pseudomonas prosekii]

Protein Classification

BRCT domain-containing protein( domain architecture ID 12947190)

BRCT (BRCA1 C-terminus) domain-containing protein may interact with DNA, and participate in DNA-damage checkpoint or DNA-repair pathways

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 ...
 3-159 1.44e-65

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: 201.97  E-value: 1.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVT-HQI 81
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGgSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1224246892  82 VASHMPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEfsQSGYGLKNLATTLGISFEHHDAVEDARAAGEILVH 159
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL--LPNHKLNTVAEHLGIELNHHDALEDARACAEILLA 156
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 197-277 4.90e-20

BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


:

Pssm-ID: 349379 [Multi-domain]  Cd Length: 76  Bit Score: 81.76  E-value: 4.90e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 197 LAGNVVVFTGAL-SIPRREAAELAASGGCEIGSGVTKHTTLLVVGDQDigrlagkdrSSKHVKAEELIAKGQNIRILGES 275
Cdd:cd17748     1 LAGKTFVFTGTLsSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNA---------GSKLKKGEELKAKGLGIKIISEE 71


                  ..
gi 1224246892 276 DF 277
Cdd:cd17748    72 EF 73
 
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 ...
 3-159 1.44e-65

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: 201.97  E-value: 1.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVT-HQI 81
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGgSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1224246892  82 VASHMPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEfsQSGYGLKNLATTLGISFEHHDAVEDARAAGEILVH 159
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL--LPNHKLNTVAEHLGIELNHHDALEDARACAEILLA 156
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-277 1.55e-47

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 161.10  E-value: 1.55e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   1 MDFTVIDVETANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDY-FHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTH 79
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  80 QIVASH-MPFDrTATLRAC---QNAGLAHFDcsWLDTARVARRTWSefSQSGYGLKNLATTLGISFEHHDAVEDARAAGE 155
Cdd:PRK06195   81 NLVIAHnASFD-ISVLRKTlelYNIPMPSFE--YICTMKLAKNFYS--NIDNARLNTVNNFLGYEFKHHDALADAMACSN 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 156 ILVHAMTHTGLT---------------AADWCSLANQPLANVLRSFNQLVINPNGE---------LAGNVVVFTGAL-SI 210
Cdd:PRK06195  156 ILLNISKELNSKdineiskllgvtlgyVNENGYKPSSRKGRILKRSNRQAPRKKKKiiesfgftaFKEEVVVFTGGLaSM 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1224246892 211 PRREAAELAASGGCEIGSGVTKHTTLLVVGDQDIGRLAGKDRSSKHVKAEELIAKGQNIRILGESDF 277
Cdd:PRK06195  236 TRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEF 302
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-161 1.14e-45

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 151.48  E-value: 1.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTH 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  80 QIVASH-MPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEFSQsgYGLKNLATTLGISF-EHHDAVEDARAAGEIL 157
Cdd:COG0847    81 AVLVAHnAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPS--YSLDALCERLGIPFdERHRALADAEATAELF 158


                  ....
gi 1224246892 158 VHAM 161
Cdd:COG0847   159 LALL 162
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-163 7.52e-28

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 105.46  E-value: 7.52e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892    3 FTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV-TH 79
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLrGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   80 QIVASH-MPFDRTATLRACQNAGL-AHFDCSWLDTARVARRTWSEFSQsgYGLKNLATTLGISFE--HHDAVEDARAAGE 155
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIkQPPKLPVIDTLKLARATNPGLPK--YSLKKLAKRLLLEVIqrAHRALDDARATAK 159


                   ....*...
gi 1224246892  156 ILVHAMTH 163
Cdd:smart00479 160 LFKKLLER 167
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 197-277 4.90e-20

BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349379 [Multi-domain]  Cd Length: 76  Bit Score: 81.76  E-value: 4.90e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 197 LAGNVVVFTGAL-SIPRREAAELAASGGCEIGSGVTKHTTLLVVGDQDigrlagkdrSSKHVKAEELIAKGQNIRILGES 275
Cdd:cd17748     1 LAGKTFVFTGTLsSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNA---------GSKLKKGEELKAKGLGIKIISEE 71


                  ..
gi 1224246892 276 DF 277
Cdd:cd17748    72 EF 73
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 5-157 2.76e-11

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: 60.83  E-value: 2.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   5 VIDVETA--NPNLASICQVGIAVFRGGKLH--QTWSSLVNPEDyFHPMN---SAVHGIDESMVASAPSWAQVYPQILPFV 77
Cdd:pfam00929   2 VIDLETTglDPEKDEIIEIAAVVIDGGENEigETFHTYVKPTR-LPKLTdecTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  78 T--HQIVASHMPFDRTATLRACQNAGLAH--FDCSWLDTARVARRTWSEFSqsGYGLKNLATTLGISF--EHHDAVEDAR 151
Cdd:pfam00929  81 RkgNLLVAHNASFDVGFLRYDDKRFLKKPmpKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHigRAHRALDDAR 158


                  ....*.
gi 1224246892 152 AAGEIL 157
Cdd:pfam00929 159 ATAKLF 164
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
194-282 3.23e-11

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 63.50  E-value: 3.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 194 NGELAGNVVVFTGALS-IPRREAAELAASGGCEIGSGVTKHTTLLVVGDQdigrlAGkdrsSKHVKAEELiakgqNIRIL 272
Cdd:COG0272   593 DSPLAGKTFVLTGTLEtMTRDEAKELIEALGGKVSGSVSKKTDYVVAGEN-----AG----SKLDKAEEL-----GVPIL 658

                          90
                  ....*....|
gi 1224246892 273 GESDFQVLLG 282
Cdd:COG0272   659 DEAEFLELLG 668
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 193-282 7.75e-11

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 62.45  E-value: 7.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 193 PNGELAGNVVVFTGALS-IPRREAAELAASGGCEIGSGVTKHTTLLVVGDQdigrlAGkdrsSKHVKAEELiakgqNIRI 271
Cdd:PRK07956  587 EEVDLAGKTVVLTGTLEqLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEA-----AG----SKLAKAQEL-----GIEV 652

                          90
                  ....*....|.
gi 1224246892 272 LGESDFQVLLG 282
Cdd:PRK07956  653 LDEEEFLRLLG 663
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 3-157 3.82e-08

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 52.84  E-value: 3.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNLA-SICQVG-IAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTHQ 80
Cdd:TIGR00573   9 ETTGDNETTGLYAGhDIIEIGaVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  81 IVASH-MPFD----RTATLRACQNAGLAHFDCSWLDTARVARRtwsEFSQSGYGLKNLATTLGISFEH---HDAVEDARA 152
Cdd:TIGR00573  89 ELVIHnASFDvgflNYEFSKLYKVEPKTNDVIDTTDTLQYARP---EFPGKRNTLDALCKRYEITNSHralHGALADAFI 165


                  ....*
gi 1224246892 153 AGEIL 157
Cdd:TIGR00573 166 LAKLY 170
 
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 ...
 3-159 1.44e-65

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: 201.97  E-value: 1.44e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVT-HQI 81
Cdd:cd06130     1 FVAIDFETANADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFLGgSLV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1224246892  82 VASHMPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEfsQSGYGLKNLATTLGISFEHHDAVEDARAAGEILVH 159
Cdd:cd06130    81 VAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRLARRVWPL--LPNHKLNTVAEHLGIELNHHDALEDARACAEILLA 156
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 1-277 1.55e-47

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 161.10  E-value: 1.55e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   1 MDFTVIDVETANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDY-FHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTH 79
Cdd:PRK06195    1 MNFVAIDFETANEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMrFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  80 QIVASH-MPFDrTATLRAC---QNAGLAHFDcsWLDTARVARRTWSefSQSGYGLKNLATTLGISFEHHDAVEDARAAGE 155
Cdd:PRK06195   81 NLVIAHnASFD-ISVLRKTlelYNIPMPSFE--YICTMKLAKNFYS--NIDNARLNTVNNFLGYEFKHHDALADAMACSN 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 156 ILVHAMTHTGLT---------------AADWCSLANQPLANVLRSFNQLVINPNGE---------LAGNVVVFTGAL-SI 210
Cdd:PRK06195  156 ILLNISKELNSKdineiskllgvtlgyVNENGYKPSSRKGRILKRSNRQAPRKKKKiiesfgftaFKEEVVVFTGGLaSM 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1224246892 211 PRREAAELAASGGCEIGSGVTKHTTLLVVGDQDIGRLAGKDRSSKHVKAEELIAKGQNIRILGESDF 277
Cdd:PRK06195  236 TRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEF 302
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 2-161 1.14e-45

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 151.48  E-value: 1.14e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTH 79
Cdd:COG0847     1 RFVVLDTETTglDPAKDRIIEIGAVKVDDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  80 QIVASH-MPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEFSQsgYGLKNLATTLGISF-EHHDAVEDARAAGEIL 157
Cdd:COG0847    81 AVLVAHnAAFDLGFLNAELRRAGLPLPPFPVLDTLRLARRLLPGLPS--YSLDALCERLGIPFdERHRALADAEATAELF 158


                  ....
gi 1224246892 158 VHAM 161
Cdd:COG0847   159 LALL 162
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-161 9.22e-37

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: 9.22e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   1 MDFTVIDVET--ANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV- 77
Cdd:COG2176     8 LTYVVFDLETtgLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLg 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  78 THQIVASHMPFDRTATLRACQNAGLAhFDCSWLDTARVARRTWSEfsQSGYGLKNLATTLGISFE-HHDAVEDARAAGEI 156
Cdd:COG2176    88 DAVLVAHNASFDLGFLNAALKRLGLP-FDNPVLDTLELARRLLPE--LKSYKLDTLAERLGIPLEdRHRALGDAEATAEL 164


                  ....*
gi 1224246892 157 LVHAM 161
Cdd:COG2176   165 FLKLL 169
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 5-157 1.19e-30

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: 112.39  E-value: 1.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   5 VIDVET--ANPNLASICQVGIAVFRGG-KLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTHQI 81
Cdd:cd06127     2 VFDTETtgLDPKKDRIIEIGAVKVDGGiEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRV 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1224246892  82 VASH-MPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEFSQSGYGLKNLATTLGISFEHHDAVEDARAAGEIL 157
Cdd:cd06127    82 LVAHnASFDLRFLNRELRRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAELL 158
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 3-163 7.52e-28

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 105.46  E-value: 7.52e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892    3 FTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV-TH 79
Cdd:smart00479   2 LVVIDCETTglDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLrGR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   80 QIVASH-MPFDRTATLRACQNAGL-AHFDCSWLDTARVARRTWSEFSQsgYGLKNLATTLGISFE--HHDAVEDARAAGE 155
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIkQPPKLPVIDTLKLARATNPGLPK--YSLKKLAKRLLLEVIqrAHRALDDARATAK 159


                   ....*...
gi 1224246892  156 ILVHAMTH 163
Cdd:smart00479 160 LFKKLLER 167
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 197-277 4.90e-20

BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349379 [Multi-domain]  Cd Length: 76  Bit Score: 81.76  E-value: 4.90e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 197 LAGNVVVFTGAL-SIPRREAAELAASGGCEIGSGVTKHTTLLVVGDQDigrlagkdrSSKHVKAEELIAKGQNIRILGES 275
Cdd:cd17748     1 LAGKTFVFTGTLsSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNA---------GSKLKKGEELKAKGLGIKIISEE 71


                  ..
gi 1224246892 276 DF 277
Cdd:cd17748    72 EF 73
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 3-162 1.30e-17

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 82.69  E-value: 1.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANpNLAS----ICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILP--- 75
Cdd:PRK08074    5 FVVVDLETTG-NSPKkgdkIIQIAAVVVEDGEILERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVElle 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  76 ---FVTHQIvashmPFDRTATLRACQNAGLAHFDCSWLDTARVARRTWSEFsqSGYGLKNLATTLGISFEH-HDAVEDAR 151
Cdd:PRK08074   84 gayFVAHNV-----HFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTA--ESYKLRDLSEELGLEHDQpHRADSDAE 156

                         170
                  ....*....|.
gi 1224246892 152 AAGEILVHAMT 162
Cdd:PRK08074  157 VTAELFLQLLN 167
polC PRK00448
DNA polymerase III PolC; Validated
 3-161 1.03e-15

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 77.19  E-value: 1.03e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892    3 FTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEdyfHPMNSAV---HGIDESMVASAPSWAQVYPQILPFV 77
Cdd:PRK00448   421 YVVFDVETTglSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPG---HPLSAFTtelTGITDDMVKDAPSIEEVLPKFKEFC 497

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   78 THQIVASH-----MPFDRTatlrACQNAGLAHFDCSWLDTARVARRTWSEFsqSGYGLKNLATTLGISFE-HHDAVEDAR 151
Cdd:PRK00448   498 GDSILVAHnasfdVGFINT----NYEKLGLEKIKNPVIDTLELSRFLYPEL--KSHRLNTLAKKFGVELEhHHRADYDAE 571

                          170
                   ....*....|
gi 1224246892  152 AAGEILVHAM 161
Cdd:PRK00448   572 ATAYLLIKFL 581
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
3-160 2.07e-15

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 76.11  E-value: 2.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVET--ANPNLASICQVGiAV-FRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTH 79
Cdd:PRK07883   17 FVVVDLETtgGSPAGDAITEIG-AVkVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARG 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  80 QI-VASHMPFDrTATLRA-CQNAGLAHFDCSWLDTARVARRTWSEFSQSGYGLKNLATTLGISFE-HHDAVEDARAAGEI 156
Cdd:PRK07883   96 AVlVAHNAPFD-IGFLRAaAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTpTHRALDDARATVDV 174


                  ....
gi 1224246892 157 LvHA 160
Cdd:PRK07883  175 L-HG 177
PRK06807 PRK06807
3'-5' exonuclease;
2-156 1.31e-13

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 69.84  E-value: 1.31e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV-T 78
Cdd:PRK06807    9 DYVVIDFETTgfNPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLhT 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1224246892  79 HQIVASHMPFDrTATLRACQNA-GLAHFDCSWLDTARVARRTWSEFSQsgYGLKNLATTLGISFEHHDAVEDARAAGEI 156
Cdd:PRK06807   89 NVIVAHNASFD-MRFLKSNVNMlGLPEPKNKVIDTVFLAKKYMKHAPN--HKLETLKRMLGIRLSSHNAFDDCITCAAV 164
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 3-161 9.12e-13

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 68.17  E-value: 9.12e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPN-LASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTHQI 81
Cdd:PRK07246    9 YAVVDLEATGAGpNASIIQVGIVIIEGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDCI 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  82 -VASHMPFDrtATLRAcQNAGLAHFD--CSWLDTARVARRTWSEFSQsgYGLKNLATTLGISFEH-HDAVEDARAAGEIL 157
Cdd:PRK07246   89 fVAHNVKFD--ANLLA-EALFLEGYElrTPRVDTVELAQVFFPTLEK--YSLSHLSRELNIDLADaHTAIADARATAELF 163


                  ....
gi 1224246892 158 VHAM 161
Cdd:PRK07246  164 LKLL 167
PRK06063 PRK06063
DEDDh family exonuclease;
2-282 2.49e-11

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 63.18  E-value: 2.49e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVETAN--PNLASIcqVGIAVFR---GGKLHQTWSSLVNPEdyFHPMNSAVHGIDESMVASAPSWAQVYPQILPF 76
Cdd:PRK06063   16 GWAVVDVETSGfrPGQARI--ISLAVLGldaDGNVEQSVVTLLNPG--VDPGPTHVHGLTAEMLEGQPQFADIAGEVAEL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  77 VTHQ-IVASHMPFDRTATLRACQNAGlAHFDCSW-LDTARVARRTwsefsqsGYGLKN-----LATTLGISFEH-HDAVE 148
Cdd:PRK06063   92 LRGRtLVAHNVAFDYSFLAAEAERAG-AELPVDQvMCTVELARRL-------GLGLPNlrletLAAHWGVPQQRpHDALD 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 149 DARAAGEILVHAMthtgLTAAD---W-----CSLANQPLANV----LRSFNQLV-------INPNGELAGNV------VV 203
Cdd:PRK06063  164 DARVLAGILRPSL----ERARErdvWlplhpVTRRRWPNGRVthdeLRPLKALAarmpcpyLNPGRYVAGRPlvqgmrVA 239

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1224246892 204 FTGALSIPRREAAELAASGGCEIGSGVTKHTTLLVVGDQDIGrlagkdrSSKHVKAEELiakgqNIRILGESDFQVLLG 282
Cdd:PRK06063  240 LSAEVSRTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPE-------QGKGYHARQL-----GVPVLDEAAFLELLR 306
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 5-157 2.76e-11

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: 60.83  E-value: 2.76e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   5 VIDVETA--NPNLASICQVGIAVFRGGKLH--QTWSSLVNPEDyFHPMN---SAVHGIDESMVASAPSWAQVYPQILPFV 77
Cdd:pfam00929   2 VIDLETTglDPEKDEIIEIAAVVIDGGENEigETFHTYVKPTR-LPKLTdecTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  78 T--HQIVASHMPFDRTATLRACQNAGLAH--FDCSWLDTARVARRTWSEFSqsGYGLKNLATTLGISF--EHHDAVEDAR 151
Cdd:pfam00929  81 RkgNLLVAHNASFDVGFLRYDDKRFLKKPmpKLNPVIDTLILDKATYKELP--GRSLDALAEKLGLEHigRAHRALDDAR 158


                  ....*.
gi 1224246892 152 AAGEIL 157
Cdd:pfam00929 159 ATAKLF 164
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
194-282 3.23e-11

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 63.50  E-value: 3.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 194 NGELAGNVVVFTGALS-IPRREAAELAASGGCEIGSGVTKHTTLLVVGDQdigrlAGkdrsSKHVKAEELiakgqNIRIL 272
Cdd:COG0272   593 DSPLAGKTFVLTGTLEtMTRDEAKELIEALGGKVSGSVSKKTDYVVAGEN-----AG----SKLDKAEEL-----GVPIL 658

                          90
                  ....*....|
gi 1224246892 273 GESDFQVLLG 282
Cdd:COG0272   659 DEAEFLELLG 668
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 3-159 4.80e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 61.77  E-value: 4.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETA--NPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVT-- 78
Cdd:PRK06310    9 FVCLDCETTglDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKeg 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  79 HQIVASHMPFDRTATLRACQNAGLAHF--DCSWLDTARVARrtwsefsqsGYG------LKNLATTLGISFE-HHDAVED 149
Cdd:PRK06310   89 DYIVGHSVGFDLQVLSQESERIGETFLskHYYIIDTLRLAK---------EYGdspnnsLEALAVHFNVPYDgNHRAMKD 159

                         170
                  ....*....|
gi 1224246892 150 ARAAGEILVH 159
Cdd:PRK06310  160 VEINIKVFKH 169
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 3-178 4.92e-11

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 61.27  E-value: 4.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNlASICQVGIAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQIL--PFVthq 80
Cdd:PRK07983    2 LRVIDTETCGLQ-GGIVEIASVDVIDGKIVNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYgsEWY--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  81 iVASHMPFDRTAtlracqnagLAHFDCSWLDTARVARRTWSEFSQSGYGLK---NLATTLGISFEHHDAVEDARAAGEIL 157
Cdd:PRK07983   78 -VAHNASFDRRV---------LPEMPGEWICTMKLARRLWPGIKYSNMALYksrKLNVQTPPGLHHHRALYDCYITAALL 147

                         170       180
                  ....*....|....*....|.
gi 1224246892 158 VHAMTHTGLTAADWCSLANQP 178
Cdd:PRK07983  148 IDIMNTSGWTAEEMADITGRP 168
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 193-282 7.75e-11

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 62.45  E-value: 7.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 193 PNGELAGNVVVFTGALS-IPRREAAELAASGGCEIGSGVTKHTTLLVVGDQdigrlAGkdrsSKHVKAEELiakgqNIRI 271
Cdd:PRK07956  587 EEVDLAGKTVVLTGTLEqLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEA-----AG----SKLAKAQEL-----GIEV 652

                          90
                  ....*....|.
gi 1224246892 272 LGESDFQVLLG 282
Cdd:PRK07956  653 LDEEEFLRLLG 663
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 197-277 1.27e-08

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 51.06  E-value: 1.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 197 LAGNVVVFTGAL-SIPRREAAELAASGGCEIGSGVTKHTTLLVVGDqDIGRlagkdrsSKHVKAEELiakgqNIRILGES 275
Cdd:cd17752     6 LEGLTFVITGVLeSLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGR-DAGP-------SKLEKAKEL-----GTKIIDED 72


                  ..
gi 1224246892 276 DF 277
Cdd:cd17752    73 GL 74
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 1-163 1.55e-08

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 53.32  E-value: 1.55e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   1 MDFTVIDVE------TANPNLAS-ICQVGIAVF-RGGKLHQTWSSLVNPEDYfhpmnSAVH-------GIDESMVASAPS 65
Cdd:COG5018     2 MKYLVIDLEatcwdgKPPPGFPMeIIEIGAVKVdENGEIIDEFSSFVKPVRR-----PKLSpfcteltGITQEDVDSAPS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  66 WAQVYPQILPFVTHQ--IVASHMPFDRTATLRACQNAGLAH-FDCSWLDTARVarrtWSEFSQSG--YGLKNLATTLGIS 140
Cdd:COG5018    77 FAEAIEDFKKWIGSEdyILCSWGDYDRKQLERNCRFHGVPYpFGDRHINLKKL----FALYFGLKkrIGLKKALELLGLE 152

                         170       180
                  ....*....|....*....|....*
gi 1224246892 141 FE--HHDAVEDARAAGEILVHAMTH 163
Cdd:COG5018   153 FEgtHHRALDDARNTAKLFKKILGD 177
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 3-157 3.82e-08

exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA]


Pssm-ID: 129663 [Multi-domain]  Cd Length: 217  Bit Score: 52.84  E-value: 3.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   3 FTVIDVETANPNLA-SICQVG-IAVFRGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFVTHQ 80
Cdd:TIGR00573   9 ETTGDNETTGLYAGhDIIEIGaVEIINRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  81 IVASH-MPFD----RTATLRACQNAGLAHFDCSWLDTARVARRtwsEFSQSGYGLKNLATTLGISFEH---HDAVEDARA 152
Cdd:TIGR00573  89 ELVIHnASFDvgflNYEFSKLYKVEPKTNDVIDTTDTLQYARP---EFPGKRNTLDALCKRYEITNSHralHGALADAFI 165


                  ....*
gi 1224246892 153 AGEIL 157
Cdd:TIGR00573 166 LAKLY 170
PRK08517 PRK08517
3'-5' exonuclease;
2-157 6.74e-08

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 52.33  E-value: 6.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVET--ANPNLASICQVGIAVFRGGKLHQTWSSLVNPEDYfhPMN-SAVHGIDESMVASAPSWAQVYPQILPFVT 78
Cdd:PRK08517   69 VFCFVDIETngSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEV--PEYiTELTGITYEDLENAPSLKEVLEEFRLFLG 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  79 HQI-VASHMPFDRTATLRACQNAGLAHFDCSWLDTARVARRTwseFSQSGYGLKNLATTLGISFE-HHDAVEDARAAGEI 156
Cdd:PRK08517  147 DSVfVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRT---IESPRYGLSFLKELLGIEIEvHHRAYADALAAYEI 223


                  .
gi 1224246892 157 L 157
Cdd:PRK08517  224 F 224
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 33-149 4.04e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 46.73  E-value: 4.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  33 QTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV-THQIVASHM--PFDRTATLRACQNAGLAHFDCSW 109
Cdd:PRK06309   33 ESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCgTDNILVAHNndAFDFPLLRKECRRHGLEPPTLRT 112

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1224246892 110 LDTARVARRTWSEFSQsgYGLKNLATTLGISFEH-HDAVED 149
Cdd:PRK06309  113 IDSLKWAQKYRPDLPK--HNLQYLRQVYGFEENQaHRALDD 151
PRK07740 PRK07740
hypothetical protein; Provisional
 1-162 6.67e-06

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 46.20  E-value: 6.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   1 MDFTVIDVETA--NPNLA-SICQVGIAVFRGGKLH-QTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPF 76
Cdd:PRK07740   59 LPFVVFDLETTgfSPQQGdEILSIGAVKTKGGEVEtDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRFYAF 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  77 VTHQI-VASHMPFDRtATLRAcqnAGLAHFDCSW----LDTARVARRTWSEfsQSGYGLKNLATTLGISFE--HHdAVED 149
Cdd:PRK07740  139 IGAGVlVAHHAGHDK-AFLRH---ALWRTYRQPFthrlIDTMFLTKLLAHE--RDFPTLDDALAYYGIPIPrrHH-ALGD 211

                         170
                  ....*....|...
gi 1224246892 150 ARAAGEILVHAMT 162
Cdd:PRK07740  212 ALMTAKLWAILLV 224
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 2-157 2.39e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 44.53  E-value: 2.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   2 DFTVIDVETA--NPNLASICQVGIAVF--RGGKLHQTWSSLVNPEDYFHPMNSAVHGIDESMVASAPSWAQVYPQILPFV 77
Cdd:PRK09146   48 PFVALDFETTglDAEQDAIVSIGLVPFtlQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERILDELLEAL 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  78 THQIVASHM-----PFDRTAtLRACQNAGLaHFDCswLDT----ARVARRT----WSEF------------SQSGYGLKn 132
Cdd:PRK09146  128 AGKVVVVHYrrierDFLDQA-LRNRIGEGI-EFPV--IDTmeieARIQRKQagglWNRLkgkkpesirladSRLRYGLP- 202

                         170       180
                  ....*....|....*....|....*
gi 1224246892 133 lattlgiSFEHHDAVEDARAAGEIL 157
Cdd:PRK09146  203 -------AYSPHHALTDAIATAELL 220
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 5-159 1.92e-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: 41.44  E-value: 1.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892   5 VIDVET------ANPNLAS-ICQVGIAVFRGGKLHQ--TWSSLVNPEDYF--HPMNSAVHGIDESMVASAPSWAQVYPQI 73
Cdd:cd06133     3 VIDFEAtcwegnSKPDYPNeIIEIGAVLVDVKTKEIidTFSSYVKPVINPklSDFCTELTGITQEDVDNAPSFPEVLKEF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  74 LPFVTHQ---IVASHMPFDRTATLRACQNAGLAHFD---CSWLDtarvARRTWSEFSQSG--YGLKNLATTLGISFE--H 143
Cdd:cd06133    83 LEWLGKNgkyAFVTWGDWDLKDLLQNQCKYKIINLPpffRQWID----LKKEFAKFYGLKkrTGLSKALEYLGLEFEgrH 158

                         170
                  ....*....|....*.
gi 1224246892 144 HDAVEDARAAGEILVH 159
Cdd:cd06133   159 HRGLDDARNIARILKR 174
BRCT_PARP1 cd17747
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ...
 197-277 6.72e-04

BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2.30), also termed ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1), or NAD(+) ADP-ribosyltransferase 1 (ADPRT 1), or poly[ADP-ribose] synthase 1, is involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism.


Pssm-ID: 349378 [Multi-domain]  Cd Length: 76  Bit Score: 37.51  E-value: 6.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892 197 LAGNVVVFTGALSIPRREAAELAASGGCEIGSGVTKHTTLLVVGDQDIgrlagkDRSSKHVKAeeliAKGQNIRILGEsD 276
Cdd:cd17747     1 LTGMKFALIGKLSKSKDELKKLIEKLGGKVASKVTKKVTLCISTKAEV------EKMSKKMKE----AKEAGVPVVSE-D 69


                  .
gi 1224246892 277 F 277
Cdd:cd17747    70 F 70
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 15-153 9.32e-04

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: 39.04  E-value: 9.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  15 LASICQVGiavFRGgklHQTWSSLVNPE----DYfhpmNSAVHGIDESMVASAPSWAQVYPQILPFVTHQIVASHmpfdr 90
Cdd:cd06144    19 LARVSIVN---EDG---NVVYDTYVKPQepvtDY----RTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGH----- 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1224246892  91 tatlracqnaGLAH-FDCSWLDTARVARR---TWSEFSQSGY----GLKNLATT-LG--ISFEHHDAVEDARAA 153
Cdd:cd06144    84 ----------ALKNdLKVLKLDHPKKLIRdtsKYKPLRKTAKgkspSLKKLAKQlLGldIQEGEHSSVEDARAA 147
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 38-157 3.65e-03

DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They 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. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.


Pssm-ID: 99848  Cd Length: 150  Bit Score: 37.08  E-value: 3.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1224246892  38 LVNPE----DYfhpmNSAVHGIDESMVASAP-SWAQVYPQILPFVTHQ-IVASH-MPFDrtatLRACQnagLAHFDCswL 110
Cdd:cd06145    33 LVKPDgeivDY----NTRFSGITEEMLENVTtTLEDVQKKLLSLISPDtILVGHsLEND----LKALK---LIHPRV--I 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1224246892 111 DTARV-ARRTWSEFSQSgygLKNLATT-LGI----SFEHHDAVEDARAAGEIL 157
Cdd:cd06145   100 DTAILfPHPRGPPYKPS---LKNLAKKyLGRdiqqGEGGHDSVEDARAALELV 149
 
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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