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Conserved domains on  [gi|487338750|gb|EOM53463|]
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exonuclease, DNA polymerase III, epsilon subunit [Enterococcus faecalis EnGen0202]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 7-176 3.25e-48

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


:

Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 158.77  E-value: 3.25e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:COG2176    9 TYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGrPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNIkSFDFPFLKA--KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAIS-HNALNDVRISAIVFME 162
Cdd:COG2176   89 AVLVAHNA-SFDLGFLNAalKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDrHRALGDAEATAELFLK 167

                        170
                 ....*....|....
gi 487338750 163 LLKIEPQEKSSTLK 176
Cdd:COG2176  168 LLEKLEEKGITTLR 181
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 193-279 7.13e-16

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: 70.97  E-value: 7.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750 193 FEGMSFVVTGAFddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQGIQISSQLKDGKhsskelkyiELREKGVDIYKFN 272
Cdd:cd17748    1 LAGKTFVFTGTL--SSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKGE---------ELKAKGLGIKIIS 69


                 ....*..
gi 487338750 273 GNQFYEL 279
Cdd:cd17748   70 EEEFLDL 76
 
Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 7-176 3.25e-48

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 158.77  E-value: 3.25e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:COG2176    9 TYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGrPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNIkSFDFPFLKA--KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAIS-HNALNDVRISAIVFME 162
Cdd:COG2176   89 AVLVAHNA-SFDLGFLNAalKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDrHRALGDAEATAELFLK 167

                        170
                 ....*....|....
gi 487338750 163 LLKIEPQEKSSTLK 176
Cdd:COG2176  168 LLEKLEEKGITTLR 181
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 9-161 3.33e-41

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: 139.74  E-value: 3.33e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   9 IAFDIETTGLDFHQDAVIQISAARYVDGIEV-DYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGDT 86
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIvERFETLVNPGrPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  87 ILVGHNIkSFDFPFLKA---KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKL-LFGIDAI-SHNALNDVRISAIVFM 161
Cdd:cd06127   81 VLVAHNA-SFDLRFLNRelrRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAeRYGIPLEgAHRALADALATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 7-166 1.12e-34

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 123.18  E-value: 1.12e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750     7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRpITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    86 TILVGHNIKSFDFPFLKA----KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTL--KLLFGIDAISHNALNDVRISAIV 159
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLehprLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLakRLLLEVIQRAHRALDDARATAKL 160


                   ....*..
gi 487338750   160 FMELLKI 166
Cdd:smart00479 161 FKKLLER 167
PRK06807 PRK06807
3'-5' exonuclease;
7-181 6.13e-31

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 117.61  E-value: 6.13e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:PRK06807   9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPErPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNiKSFDFPFLKAKGYNIAEG---HEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAISHNALNDVRISAIVFME 162
Cdd:PRK06807  89 NVIVAHN-ASFDMRFLKSNVNMLGLPepkNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCAAVYQK 167

                        170
                 ....*....|....*....
gi 487338750 163 LLKIEpQEKSSTLKKSSLD 181
Cdd:PRK06807 168 CASIE-EEAKRKSNKEVLD 185
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 9-160 2.24e-21

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 88.18  E-value: 2.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    9 IAFDIETTGLDFHQDAVIQISAARYVDGI--EVDYFDTLVN---SDYIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYL 83
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKptrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   84 G-DTILVGHNiKSFDFPFLKAK-----GYNIAEGHEIYDTRYFA-ATRKhGAVNNQLTTL--KLLFGIDAISHNALNDVR 154
Cdd:pfam00929  81 RkGNLLVAHN-ASFDVGFLRYDdkrflKKPMPKLNPVIDTLILDkATYK-ELPGRSLDALaeKLGLEHIGRAHRALDDAR 158


                  ....*.
gi 487338750  155 ISAIVF 160
Cdd:pfam00929 159 ATAKLF 164
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 193-279 7.13e-16

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: 70.97  E-value: 7.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750 193 FEGMSFVVTGAFddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQGIQISSQLKDGKhsskelkyiELREKGVDIYKFN 272
Cdd:cd17748    1 LAGKTFVFTGTL--SSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKGE---------ELKAKGLGIKIIS 69


                 ....*..
gi 487338750 273 GNQFYEL 279
Cdd:cd17748   70 EEEFLDL 76
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 2-165 2.38e-13

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: 67.48  E-value: 2.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    2 QTEVKEFIAFDIETTGLDFHQDaVIQISAARYVDG-IEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYL 79
Cdd:TIGR00573   3 QLVLDTETTGDNETTGLYAGHD-IIEIGAVEIINRrITGNKFHTYIKPDRpIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   80 FDYLGDTILVGHNIkSFDFPFLKAK----GYNIAEGHEIYDTRYFAATRKHGAVNNQLTT--LKLLFGIDaISHNALNDV 153
Cdd:TIGR00573  82 ADYIRGAELVIHNA-SFDVGFLNYEfsklYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLdaLCKRYEIT-NSHRALHGA 159

                         170
                  ....*....|..
gi 487338750  154 RISAIVFMELLK 165
Cdd:TIGR00573 160 LADAFILAKLYL 171
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
193-239 9.31e-11

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 61.96  E-value: 9.31e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 487338750 193 FEGMSFVVTGAFddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQG 239
Cdd:COG0272  596 LAGKTFVLTGTL--ETMTRDEAKELIEALGGKVSGSVSKKTDYVVAG 640
BRCT smart00292
breast cancer carboxy-terminal domain;
191-271 4.18e-07

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 46.60  E-value: 4.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   191 PFFEGMSFVVTGAFDdsKYNRKQIETLIKQHGGRVSSSLSAK-TDYFIQgiqissqlkdGKHSSKELKYIELREKGVDIY 269
Cdd:smart00292   2 KLFKGKTFYITGSFD--KEERDELKELIEALGGKVTSSLSSKtTTHVIV----------GSPEGGKLELLKAIALGIPIV 69


                   ..
gi 487338750   270 KF 271
Cdd:smart00292  70 KE 71
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 175-239 1.64e-06

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 48.98  E-value: 1.64e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 487338750 175 LKKSSLDSFELDDDTTPFFEGMSFVVTGAFDDskYNRKQIETLIKQHGGRVSSSLSAKTDYFIQG 239
Cdd:PRK14351 592 LLDHGVDPQPAESEGGDALDGLTFVFTGSLSG--YTRSEAQELVEAHGGNATGSVSGNTDYLVVG 654
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 191-237 5.17e-06

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 43.44  E-value: 5.17e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 487338750  191 PFFEGMSFVVTGafdDSKYNRKQIETLIKQHGGRVSSSLSAKTDYFI 237
Cdd:pfam00533   4 KLFSGKTFVITG---LDGLERDELKELIEKLGGKVTDSLSKKTTHVI 47
 
Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 7-176 3.25e-48

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 158.77  E-value: 3.25e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:COG2176    9 TYVVFDLETTGLSPKKDEIIEIGAVKVENGEIVDRFSTLVNPGrPIPPFITELTGITDEMVADAPPFEEVLPEFLEFLGD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNIkSFDFPFLKA--KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAIS-HNALNDVRISAIVFME 162
Cdd:COG2176   89 AVLVAHNA-SFDLGFLNAalKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDrHRALGDAEATAELFLK 167

                        170
                 ....*....|....
gi 487338750 163 LLKIEPQEKSSTLK 176
Cdd:COG2176  168 LLEKLEEKGITTLR 181
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 7-165 1.63e-44

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 148.40  E-value: 1.63e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVDDGRIVETFHTLVNPErPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNIkSFDFPFLKA--KGYNIAE-GHEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAI-SHNALNDVRISAIVFM 161
Cdd:COG0847   81 AVLVAHNA-AFDLGFLNAelRRAGLPLpPFPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDeRHRALADAEATAELFL 159


                 ....
gi 487338750 162 ELLK 165
Cdd:COG0847  160 ALLR 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 9-161 3.33e-41

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: 139.74  E-value: 3.33e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   9 IAFDIETTGLDFHQDAVIQISAARYVDGIEV-DYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGDT 86
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIvERFETLVNPGrPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  87 ILVGHNIkSFDFPFLKA---KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKL-LFGIDAI-SHNALNDVRISAIVFM 161
Cdd:cd06127   81 VLVAHNA-SFDLRFLNRelrRLGGPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAeRYGIPLEgAHRALADALATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 7-166 1.12e-34

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 123.18  E-value: 1.12e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750     7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:smart00479   1 TLVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRpITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    86 TILVGHNIKSFDFPFLKA----KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTL--KLLFGIDAISHNALNDVRISAIV 159
Cdd:smart00479  81 RILVAGNSAHFDLRFLKLehprLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLakRLLLEVIQRAHRALDDARATAKL 160


                   ....*..
gi 487338750   160 FMELLKI 166
Cdd:smart00479 161 FKKLLER 167
PRK06807 PRK06807
3'-5' exonuclease;
7-181 6.13e-31

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 117.61  E-value: 6.13e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSD-YIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:PRK06807   9 DYVVIDFETTGFNPYNDKIIQVAAVKYRNHELVDQFVSYVNPErPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFLHT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNiKSFDFPFLKAKGYNIAEG---HEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAISHNALNDVRISAIVFME 162
Cdd:PRK06807  89 NVIVAHN-ASFDMRFLKSNVNMLGLPepkNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCAAVYQK 167

                        170
                 ....*....|....*....
gi 487338750 163 LLKIEpQEKSSTLKKSSLD 181
Cdd:PRK06807 168 CASIE-EEAKRKSNKEVLD 185
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
8-164 1.50e-26

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 108.47  E-value: 1.50e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVN-SDYIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGDT 86
Cdd:PRK07883  17 FVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNpGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFARGA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  87 ILVGHNIkSFDFPFLKAKgyniAEGHEI-------YDTRYFAAT--RKHGAVNNQLTTLKLLFGID-AISHNALNDVRIS 156
Cdd:PRK07883  97 VLVAHNA-PFDIGFLRAA----AARCGYpwpgppvLCTVRLARRvlPRDEAPNVRLSTLARLFGATtTPTHRALDDARAT 171


                 ....*...
gi 487338750 157 AIVFMELL 164
Cdd:PRK07883 172 VDVLHGLI 179
PRK07247 PRK07247
3'-5' exonuclease;
7-163 1.61e-26

3'-5' exonuclease;


Pssm-ID: 180906 [Multi-domain]  Cd Length: 195  Bit Score: 102.94  E-value: 1.61e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDfHQDAVIQISAARYVDGIEVDYFDTLVNSDyIPDE--ITKLTGITNDQVLNAPTLDEVMPYLFDYLG 84
Cdd:PRK07247   6 TYIAFDLEFNTVN-GVSHIIQVSAVKYDDHKEVDSFDSYVYTD-VPLQsfINGLTGITADKIADAPKVEEVLAAFKEFVG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  85 DTILVGHNIKSFDFPFLKAKGYNIAEGHEI--YDTRY-FAATRKHGAVNNQLTTLKLLFGIDAISHNALNDVRISAIV-- 159
Cdd:PRK07247  84 ELPLIGYNAQKSDLPILAENGLDLSDQYQVdlYDEAFeRRSSDLNGIANLKLQTVADFLGIKGRGHNSLEDARMTARVye 163


                 ....*
gi 487338750 160 -FMEL 163
Cdd:PRK07247 164 sFLES 168
polC PRK00448
DNA polymerase III PolC; Validated
 7-165 4.43e-25

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 104.92  E-value: 4.43e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:PRK00448  420 TYVVFDVETTGLSAVYDEIIEIGAVKIKNGEIIDKFEFFIKPGHpLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGD 499

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   86 TILVGHNiKSFDFPFLKA--KGYNIAEGHEIY-DTRYFAAT-----RKHGavnnqLTTLKLLFGIDAIS-HNALNDVRIS 156
Cdd:PRK00448  500 SILVAHN-ASFDVGFINTnyEKLGLEKIKNPViDTLELSRFlypelKSHR-----LNTLAKKFGVELEHhHRADYDAEAT 573


                  ....*....
gi 487338750  157 AIVFMELLK 165
Cdd:PRK00448  574 AYLLIKFLK 582
PRK08517 PRK08517
3'-5' exonuclease;
2-174 4.05e-22

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 92.39  E-value: 4.05e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   2 QTEVKE--FIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSDYIPDEITKLTGITNDQVLNAPTLDEVMPYL 79
Cdd:PRK08517  62 FTPIKDqvFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  80 FDYLGDTILVGHNIKsFDFPFLKAKGYNIaeGHEIYDTRYFA----ATRKHGAVNNQLTTLKLLFGID-AISHNALNDVR 154
Cdd:PRK08517 142 RLFLGDSVFVAHNVN-FDYNFISRSLEEI--GLGPLLNRKLCtidlAKRTIESPRYGLSFLKELLGIEiEVHHRAYADAL 218

                        170       180
                 ....*....|....*....|
gi 487338750 155 ISAIVFMELLKIEPQEKSST 174
Cdd:PRK08517 219 AAYEIFKICLLNLPSYIKTT 238
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 9-160 2.24e-21

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 88.18  E-value: 2.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    9 IAFDIETTGLDFHQDAVIQISAARYVDGI--EVDYFDTLVN---SDYIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYL 83
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIDGGEneIGETFHTYVKptrLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   84 G-DTILVGHNiKSFDFPFLKAK-----GYNIAEGHEIYDTRYFA-ATRKhGAVNNQLTTL--KLLFGIDAISHNALNDVR 154
Cdd:pfam00929  81 RkGNLLVAHN-ASFDVGFLRYDdkrflKKPMPKLNPVIDTLILDkATYK-ELPGRSLDALaeKLGLEHIGRAHRALDDAR 158


                  ....*.
gi 487338750  155 ISAIVF 160
Cdd:pfam00929 159 ATAKLF 164
PRK07740 PRK07740
hypothetical protein; Provisional
 7-176 8.80e-21

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 88.57  E-value: 8.80e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGldF---HQDAVIQISAARYVDG-IEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFD 81
Cdd:PRK07740  60 PFVVFDLETTG--FspqQGDEILSIGAVKTKGGeVETDTFYSLVKPKRpIPEHILELTGITAEDVAFAPPLAEVLHRFYA 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  82 YLGDTILVGHNIkSFDFPFLKA---KGYNIAEGHEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAIS-HNALNDVRISA 157
Cdd:PRK07740 138 FIGAGVLVAHHA-GHDKAFLRHalwRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRrHHALGDALMTA 216

                        170
                 ....*....|....*....
gi 487338750 158 IVFMELLKIEPQEKSSTLK 176
Cdd:PRK07740 217 KLWAILLVEAQQRGITTLH 235
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 8-157 1.39e-20

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: 86.03  E-value: 1.39e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETTglDFHQDAVIQISAARYVDGIEVDYFDTLVNSDYIPDEI-TKLTGITNDQVLNAPTLDEVMPYLFDYLGDT 86
Cdd:cd06130    1 FVAIDFETA--NADRASACSIGLVKVRDGQIVDTFYTLIRPPTRFDPFnIAIHGITPEDVADAPTFPEVWPEIKPFLGGS 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 487338750  87 ILVGHNIkSFDFPFLKA--KGYNIAEGHEIY-DTRYFAatRKH--GAVNNQLTTLKLLFGIDAISHNALNDVRISA 157
Cdd:cd06130   79 LVVAHNA-SFDRSVLRAalEAYGLPPPPYQYlCTVRLA--RRVwpLLPNHKLNTVAEHLGIELNHHDALEDARACA 151
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 9-163 4.71e-20

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: 84.89  E-value: 4.71e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   9 IAFDIETTGLDFHQ-DAVIQISAARYVDGIEVD-YFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:cd06131    2 IVLDTETTGLDPREgHRIIEIGCVELINRRLTGnTFHVYINPERdIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 TILVGHNIkSFDFPFLKA------KGYNIAEGHEIYDTRYFAATRKHGAVNNqLTTLKLLFGIDAIS---HNALNDVRIS 156
Cdd:cd06131   82 AELVIHNA-SFDVGFLNAelsllgLGKKIIDFCRVIDTLALARKKFPGKPNS-LDALCKRFGIDNSHrtlHGALLDAELL 159


                 ....*..
gi 487338750 157 AIVFMEL 163
Cdd:cd06131  160 AEVYLEL 166
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 7-165 1.74e-17

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 79.87  E-value: 1.74e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDGIEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGD 85
Cdd:PRK06310   8 EFVCLDCETTGLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERvVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFFKE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  86 T-ILVGHNIkSFDFPFLKAKGYNIAE-----GHEIYDTRYFAatRKHG-AVNNQLTTLKLLFGIDA-ISHNALNDVRISA 157
Cdd:PRK06310  88 GdYIVGHSV-GFDLQVLSQESERIGEtflskHYYIIDTLRLA--KEYGdSPNNSLEALAVHFNVPYdGNHRAMKDVEINI 164


                 ....*...
gi 487338750 158 IVFMELLK 165
Cdd:PRK06310 165 KVFKHLCK 172
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 9-178 5.81e-17

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 77.93  E-value: 5.81e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   9 IAFDIETTGLDFHQDAVIQISAaryVDGIEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLG-DT 86
Cdd:PRK06309   5 IFYDTETTGTQIDKDRIIEIAA---YNGVTSESFQTLVNPEIpIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGtDN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  87 ILVGHNIKSFDFPFLKAKgyniAEGHEI-------YDTRYFAATRKHGAVNNQLTTLKLLFGIDA-ISHNALNDVRISAI 158
Cdd:PRK06309  82 ILVAHNNDAFDFPLLRKE----CRRHGLepptlrtIDSLKWAQKYRPDLPKHNLQYLRQVYGFEEnQAHRALDDVITLHR 157

                        170       180
                 ....*....|....*....|.
gi 487338750 159 VFMELL-KIEPQEKSSTLKKS 178
Cdd:PRK06309 158 VFSALVgDLSPQQVYDLLNES 178
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 8-280 8.06e-17

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 79.05  E-value: 8.06e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETTglDFHQDAVIQISAARYVDGIEVDYFDTLVNSD---YIPDEItKLTGITNDQVLNAPTLDEVMPYLFDYLG 84
Cdd:PRK06195   3 FVAIDFETA--NEKRNSPCSIGIVVVKDGEIVEKVHYLIKPKemrFMPINI-GIHGIRPHMVEDELEFDKIWEKIKHYFN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  85 DTILVGHNiKSFDFPFLKA--KGYNiaegHEIYDTRYfAATRK------HGAVNNQLTTLKLLFGIDAISHNALNDVRIS 156
Cdd:PRK06195  80 NNLVIAHN-ASFDISVLRKtlELYN----IPMPSFEY-ICTMKlaknfySNIDNARLNTVNNFLGYEFKHHDALADAMAC 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750 157 AIVFM---ELLKIE-----------------------PQEKSSTLKKSSLDSFELDDDTTPFFEGMSF-----VVTGAFd 205
Cdd:PRK06195 154 SNILLnisKELNSKdineiskllgvtlgyvnengykpSSRKGRILKRSNRQAPRKKKKIIESFGFTAFkeevvVFTGGL- 232

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 487338750 206 dSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQGIQISSQLKDGKHSSKELKYIELREKGVDIYKFNGNQFYELI 280
Cdd:PRK06195 233 -ASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKFLNEEEFLQKC 306
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 6-167 1.60e-16

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 79.61  E-value: 1.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   6 KEFIAFDIETTGldfHQ----DAVIQISAARYVDGIEVDYFDTLVN-SDYIPDEITKLTGITNDQVLNAPTLDEVMPYLF 80
Cdd:PRK08074   3 KRFVVVDLETTG---NSpkkgDKIIQIAAVVVEDGEILERFSSFVNpERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  81 DYLGDTILVGHNIkSFDFPFLKAK----GYNIAEGhEIYDTRYFAATRKHGAVNNQLTTLKLLFGIDAIS-HNALNDVRI 155
Cdd:PRK08074  80 ELLEGAYFVAHNV-HFDLNFLNEEleraGYTEIHC-PKLDTVELARILLPTAESYKLRDLSEELGLEHDQpHRADSDAEV 157

                        170
                 ....*....|...
gi 487338750 156 SAIVFMELL-KIE 167
Cdd:PRK08074 158 TAELFLQLLnKLE 170
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 193-279 7.13e-16

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: 70.97  E-value: 7.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750 193 FEGMSFVVTGAFddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQGIQISSQLKDGKhsskelkyiELREKGVDIYKFN 272
Cdd:cd17748    1 LAGKTFVFTGTL--SSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKGE---------ELKAKGLGIKIIS 69


                 ....*..
gi 487338750 273 GNQFYEL 279
Cdd:cd17748   70 EEEFLDL 76
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 2-165 2.38e-13

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: 67.48  E-value: 2.38e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    2 QTEVKEFIAFDIETTGLDFHQDaVIQISAARYVDG-IEVDYFDTLVNSDY-IPDEITKLTGITNDQVLNAPTLDEVMPYL 79
Cdd:TIGR00573   3 QLVLDTETTGDNETTGLYAGHD-IIEIGAVEIINRrITGNKFHTYIKPDRpIDPDAIKIHGITDDMLKDKPDFKEIAEDF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   80 FDYLGDTILVGHNIkSFDFPFLKAK----GYNIAEGHEIYDTRYFAATRKHGAVNNQLTT--LKLLFGIDaISHNALNDV 153
Cdd:TIGR00573  82 ADYIRGAELVIHNA-SFDVGFLNYEfsklYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLdaLCKRYEIT-NSHRALHGA 159

                         170
                  ....*....|..
gi 487338750  154 RISAIVFMELLK 165
Cdd:TIGR00573 160 LADAFILAKLYL 171
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
193-239 9.31e-11

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 61.96  E-value: 9.31e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 487338750 193 FEGMSFVVTGAFddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFIQG 239
Cdd:COG0272  596 LAGKTFVLTGTL--ETMTRDEAKELIEALGGKVSGSVSKKTDYVVAG 640
PRK06063 PRK06063
DEDDh family exonuclease;
12-160 1.84e-09

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 57.40  E-value: 1.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  12 DIETTGLDFHQDAVIqiSAARYV---DGIEVDYFDTLVNSDYIPDEiTKLTGITNDQVLNAPTLDEVMPYLFDYLGDTIL 88
Cdd:PRK06063  21 DVETSGFRPGQARII--SLAVLGldaDGNVEQSVVTLLNPGVDPGP-THVHGLTAEMLEGQPQFADIAGEVAELLRGRTL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 487338750  89 VGHNIkSFDFPFLKAKgYNIAEGHEIYDTRY--FAATRK--HGAVNNQLTTLKLLFGIDAI-SHNALNDVRISAIVF 160
Cdd:PRK06063  98 VAHNV-AFDYSFLAAE-AERAGAELPVDQVMctVELARRlgLGLPNLRLETLAAHWGVPQQrPHDALDDARVLAGIL 172
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 8-164 3.50e-09

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: 54.92  E-value: 3.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETT------GLDFHQDaVIQISAARYVD--GIEVDYFDTLVNSDYIP---DEITKLTGITNDQVLNAPTLDEVM 76
Cdd:cd06133    1 YLVIDFEATcwegnsKPDYPNE-IIEIGAVLVDVktKEIIDTFSSYVKPVINPklsDFCTELTGITQEDVDNAPSFPEVL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  77 PYLFDYLGD---------------TILVGHNIKSFDFPFLKAKGY-NIAeghEIYDTRYfaATRKHGAVNNQLTTLKLLF 140
Cdd:cd06133   80 KEFLEWLGKngkyafvtwgdwdlkDLLQNQCKYKIINLPPFFRQWiDLK---KEFAKFY--GLKKRTGLSKALEYLGLEF 154

                        170       180
                 ....*....|....*....|....
gi 487338750 141 giDAISHNALNDVRISAIVFMELL 164
Cdd:cd06133  155 --EGRHHRGLDDARNIARILKRLL 176
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 193-239 3.91e-09

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: 52.60  E-value: 3.91e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 487338750 193 FEGMSFVVTGAFDDSKynRKQIETLIKQHGGRVSSSLSAKTDYFIQG 239
Cdd:cd17752    6 LEGLTFVITGVLESLE--REEAEDLIKRYGGKVTGSVSKKTSYLVVG 50
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 1-182 8.45e-09

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 56.23  E-value: 8.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   1 MQTEVKEFIAFDIETTGLDfHQDAVIQISAARYVDGIEVDYFDTLVNS-DYIPDEITKLTGITNDQVLNAPTLDEVMPYL 79
Cdd:PRK07246   2 TQKKLRKYAVVDLEATGAG-PNASIIQVGIVIIEGGEIIDSYTTDVNPhEPLDEHIKHLTGITDQQLAQAPDFSQVARHI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  80 FDYLGDTILVGHNIKsFDFPFLKAKGYniAEGHEIYDTR---------YFAATRKHgavnnQLTTLKLLFGID-AISHNA 149
Cdd:PRK07246  81 YDLIEDCIFVAHNVK-FDANLLAEALF--LEGYELRTPRvdtvelaqvFFPTLEKY-----SLSHLSRELNIDlADAHTA 152

                        170       180       190
                 ....*....|....*....|....*....|...
gi 487338750 150 LNDVRISAIVFMELLkiepqEKSSTLKKSSLDS 182
Cdd:PRK07246 153 IADARATAELFLKLL-----QKIESLPKECLER 180
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 8-165 3.51e-08

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 52.17  E-value: 3.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETTGLD------FHQDaVIQISAARY-VDGIEVDYFDTLV----NSDyIPDEITKLTGITNDQVLNAPTLDEVM 76
Cdd:COG5018    4 YLVIDLEATCWDgkpppgFPME-IIEIGAVKVdENGEIIDEFSSFVkpvrRPK-LSPFCTELTGITQEDVDSAPSFAEAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  77 PYLFDYLG--DTILV--GHN----------IKSFDFPFLKaKGYNIAEGHeiydTRYFAATRKHGaVNNQLTTLKLLFGI 142
Cdd:COG5018   82 EDFKKWIGseDYILCswGDYdrkqlerncrFHGVPYPFGD-RHINLKKLF----ALYFGLKKRIG-LKKALELLGLEFEG 155

                        170       180
                 ....*....|....*....|...
gi 487338750 143 DAisHNALNDVRISAIVFMELLK 165
Cdd:COG5018  156 TH--HRALDDARNTAKLFKKILG 176
YprB COG3359
Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function ...
 4-143 1.92e-07

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


Pssm-ID: 442587 [Multi-domain]  Cd Length: 198  Bit Score: 50.33  E-value: 1.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   4 EVKEFIAFDIETTGLDFHQDAVIQISAARYVDGIEVdyFDTLVNSDyIPDEitkltgitndqvlnAPTLDEVMPYLFDYl 83
Cdd:COG3359   13 PSEDLLFFDIETTGLSGGGTVIFLIGLADGEGDGFV--VRQYFGED-PGEE--------------AALLEAFLEWLADY- 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 487338750  84 gdTILVGHNIKSFDFPFLKAK--GYNI---AEGHEIYDTRYFAATR-KHGAVNNQLTTLKLLFGID 143
Cdd:COG3359   75 --KLLVTYNGKSFDLPFLKTRftLHRLpppLPEFPHLDLLHPARRLwKNRLPSGGLKTVEELLGIE 138
DNA_pol_B_exo1 pfam03104
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ...
 9-186 2.23e-07

DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.


Pssm-ID: 397292  Cd Length: 333  Bit Score: 51.26  E-value: 2.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750    9 IAFDIETTGLD-------FHQDAVIQISAARYVDGIEVDYFD---TLVNSDYIPD---EITKLTGITNDQVLNAPTLDEV 75
Cdd:pfam03104 158 LSFDIECTSLPgkfpdaeNVKDPIIQISCMLDGQGEPEPEPRflfTLRECDSEDIedfEYTPKPIYPGVKVFEFPSEKEL 237

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   76 MPYLFDYLGD---TILVGHNIKSFDFPFLKAKgyniAEGHEIYDTRYFAATRKHGAVNNQlttlKLLFGIDAISHnalnd 152
Cdd:pfam03104 238 LRRFFEFIRQydpDIITGYNGDNFDWPYILNR----AKELYIVKLSSIGRLNRGGRSKVR----EIGFGTRSYEK----- 304

                         170       180       190
                  ....*....|....*....|....*....|....
gi 487338750  153 VRISAIVFMELLKIepqekssTLKKSSLDSFELD 186
Cdd:pfam03104 305 VKISGRLHLDLYRV-------IKRDYKLPSYKLN 331
BRCT smart00292
breast cancer carboxy-terminal domain;
191-271 4.18e-07

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 46.60  E-value: 4.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   191 PFFEGMSFVVTGAFDdsKYNRKQIETLIKQHGGRVSSSLSAK-TDYFIQgiqissqlkdGKHSSKELKYIELREKGVDIY 269
Cdd:smart00292   2 KLFKGKTFYITGSFD--KEERDELKELIEALGGKVTSSLSSKtTTHVIV----------GSPEGGKLELLKAIALGIPIV 69


                   ..
gi 487338750   270 KF 271
Cdd:smart00292  70 KE 71
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 12-103 8.91e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 49.20  E-value: 8.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  12 DIETTGLDFHQDAVIQIS--AARY-VDGIEVDYFDTLVN----SDYIPDEITKLTGITNDQVLNApTLDevMPYLFDYLG 84
Cdd:PRK09182  43 DTETTGLDPRKDEIIEIGmvAFEYdDDGRIGDVLDTFGGlqqpSRPIPPEITRLTGITDEMVAGQ-TID--PAAVDALIA 119

                         90       100
                 ....*....|....*....|
gi 487338750  85 DT-ILVGHNiKSFDFPFLKA 103
Cdd:PRK09182 120 PAdLIIAHN-AGFDRPFLER 138
PRK09145 PRK09145
3'-5' exonuclease;
7-101 1.38e-06

3'-5' exonuclease;


Pssm-ID: 236391 [Multi-domain]  Cd Length: 202  Bit Score: 47.97  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAARYVDG--IEVDYFDTLVNSDYIPDEIT-KLTGITNDQVLNAPTLDEVMPYLFDYL 83
Cdd:PRK09145  30 EWVALDCETTGLDPRRAEIVSIAAVKIRGNriLTSERLELLVRPPQSLSAESiKIHRLRHQDLEDGLSEEEALRQLLAFI 109

                         90
                 ....*....|....*...
gi 487338750  84 GDTILVGHNIkSFDFPFL 101
Cdd:PRK09145 110 GNRPLVGYYL-EFDVAML 126
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 175-239 1.64e-06

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 48.98  E-value: 1.64e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 487338750 175 LKKSSLDSFELDDDTTPFFEGMSFVVTGAFDDskYNRKQIETLIKQHGGRVSSSLSAKTDYFIQG 239
Cdd:PRK14351 592 LLDHGVDPQPAESEGGDALDGLTFVFTGSLSG--YTRSEAQELVEAHGGNATGSVSGNTDYLVVG 654
DEDDy_DNA_polB_exo cd05160
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ...
 8-102 1.74e-06

DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.


Pssm-ID: 176646 [Multi-domain]  Cd Length: 199  Bit Score: 47.74  E-value: 1.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   8 FIAFDIETT----GLDFHQDAVIQISAARYVDGieVDYFDTLVNSDYIPDEitklTGITNDQVLNAPTLDEVMPYLFDYL 83
Cdd:cd05160    1 VLSFDIETTppvgGPEPDRDPIICITYADSFDG--VKVVFLLKTSTVGDDI----EFIDGIEVEYFADEKELLKRFFDII 74

                         90       100
                 ....*....|....*....|..
gi 487338750  84 GDT---ILVGHNIKSFDFPFLK 102
Cdd:cd05160   75 REYdpdILTGYNIDDFDLPYLL 96
RNase_H_2 pfam13482
RNase_H superfamily;
11-127 3.82e-06

RNase_H superfamily;


Pssm-ID: 433246 [Multi-domain]  Cd Length: 163  Bit Score: 46.05  E-value: 3.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   11 FDIETTGLDFHQDAVIQISAARyVDGIEVDYFDTLVNSDyipdeitkltgitndqvlnaPTLDEVMPYLFDYLGD-TILV 89
Cdd:pfam13482   3 FDIETTGLSPGKNTIYLIGVYD-VDGDKVRTFVQYLAEG--------------------PTEEAAILQLFELLADyPLLV 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 487338750   90 GHNIKSFDFPFLK--AKGYNIAEGHEIYDTRYFAatRKHG 127
Cdd:pfam13482  62 TFNGKSFDVPFIKrrFKRYDLDELFRHIDLLHPL--RKLG 99
BRCT_PARP1 cd17747
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ...
 193-268 4.73e-06

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: 43.67  E-value: 4.73e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 487338750 193 FEGMSFVVTGAFDDSKynrKQIETLIKQHGGRVSSSLSAKTDYFiqgiqISSQLKDGKHSSkelKYIELREKGVDI 268
Cdd:cd17747    1 LTGMKFALIGKLSKSK---DELKKLIEKLGGKVASKVTKKVTLC-----ISTKAEVEKMSK---KMKEAKEAGVPV 65
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 191-237 5.17e-06

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 43.44  E-value: 5.17e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 487338750  191 PFFEGMSFVVTGafdDSKYNRKQIETLIKQHGGRVSSSLSAKTDYFI 237
Cdd:pfam00533   4 KLFSGKTFVITG---LDGLERDELKELIEKLGGKVTDSLSKKTTHVI 47
BRCT_p53bp1_rpt1 cd17745
first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 192-225 8.87e-06

first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain.


Pssm-ID: 349376 [Multi-domain]  Cd Length: 99  Bit Score: 43.45  E-value: 8.87e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 487338750 192 FFEGMSFVVTGAFDDSK-YNRKQIETLIKQHGGRV 225
Cdd:cd17745    1 IFSGCAFLLTGAEETDKpFDKERLESQIEANGGTV 35
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 7-91 3.54e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 44.15  E-value: 3.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQI------------SAARYvdgievdyfdTLVN-SDYIPDEITKLTGITNDQVLNAPTLD 73
Cdd:PRK09146  48 PFVALDFETTGLDAEQDAIVSIglvpftlqrircRQARH----------WVVKpRRPLEEESVVIHGITHSELQDAPDLE 117

                         90
                 ....*....|....*...
gi 487338750  74 EVMPYLFDYLGDTILVGH 91
Cdd:PRK09146 118 RILDELLEALAGKVVVVH 135
BRCT_TopBP1_rpt2_like cd17731
second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; ...
 191-230 4.39e-05

second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the second BRCT domain.


Pssm-ID: 349363 [Multi-domain]  Cd Length: 77  Bit Score: 40.99  E-value: 4.39e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 487338750 191 PFFEGMSFVVTGaFDDSKynRKQIETLIKQHGGRVSSSLS 230
Cdd:cd17731    1 PPFKGLVICVTG-FDSEE--RKEIQQLVEQNGGSYSPDLS 37
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 6-146 4.70e-05

DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D 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 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.


Pssm-ID: 176651 [Multi-domain]  Cd Length: 193  Bit Score: 43.28  E-value: 4.70e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   6 KEFIAFDIETTGLDFHQDAVIQISAAryvdgievdyfdtlVNSD---YIPdeitkLTGITNDQVLNaptLDEVMPYLFDY 82
Cdd:cd06139    5 AKVFAFDTETTSLDPMQAELVGISFA--------------VEPGeayYIP-----LGHDYGGEQLP---REEVLAALKPL 62

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 487338750  83 LGD-TIL-VGHNIKsFDFPFLKAkgYNIAEGHEIYDTR-----YFAATRKHGavnnqLTTL-KLLFGIDAIS 146
Cdd:cd06139   63 LEDpSIKkVGQNLK-FDLHVLAN--HGIELRGPAFDTMlasylLNPGRRRHG-----LDDLaERYLGHKTIS 126
REX1_like cd06145
DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins; This ...
 39-91 5.80e-05

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: 42.47  E-value: 5.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 487338750  39 VDY-----FDTLVNSDY-IPDEITKLTGITNDQVLNAP-TLDEVMPYLFDYLG-DTILVGH 91
Cdd:cd06145   22 VDEngkvvLDELVKPDGeIVDYNTRFSGITEEMLENVTtTLEDVQKKLLSLISpDTILVGH 82
BRCT_DNA_ligase_IV_rpt1 cd17722
first BRCT domain of DNA ligase 4 (LIG4) and similar proteins; LIG4 (EC 6.5.1.1), also termed ...
 193-251 8.58e-05

first BRCT domain of DNA ligase 4 (LIG4) and similar proteins; LIG4 (EC 6.5.1.1), also termed DNA ligase IV, or polydeoxyribonucleotide synthase [ATP] 4, is involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. It is a component of the LIG4-XRCC4 complex that is responsible for the NHEJ ligation step. LIG4 contains two BRCT domains. The family corresponds to the first one.


Pssm-ID: 349354 [Multi-domain]  Cd Length: 90  Bit Score: 40.36  E-value: 8.58e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 487338750 193 FEGMSFVVTgAFDDSKYNRKQIETLIKQHGGRVSSSLSAKTDYFI----QGIQISSQLKDGKH 251
Cdd:cd17722    2 FEGVEFCVM-SDMSSPKSKAELEKLIKENGGKVVQNPGAPDTICViagrEVVKVKNLIKSGGH 63
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
 189-237 3.52e-04

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 38.50  E-value: 3.52e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 487338750  189 TTPFFEGMSFVVTGAfddSKYNRKQIETLIKQHGGRVSSSLSAKTDYFI 237
Cdd:pfam16589   1 LPNLFEPLRFYINAI---PSPSRSKLKRLIEANGGTVVDNINPAVYIVI 46
REX4_like cd06144
DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product ...
 39-154 1.91e-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: 37.88  E-value: 1.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750  39 VDY-----FDTLVN-SDYIPDEITKLTGITNDQVLNAPTLDEVMPYLFDYLGDTILVGHNIKSfDFPFLKAKgyniAEGH 112
Cdd:cd06144   25 VNEdgnvvYDTYVKpQEPVTDYRTAVSGIRPEHLKDAPDFEEVQKKVAELLKGRILVGHALKN-DLKVLKLD----HPKK 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 487338750 113 EIYDT-RYFAATRKHGAVNNQLTTL-KLLFGIDaI---SHNALNDVR 154
Cdd:cd06144  100 LIRDTsKYKPLRKTAKGKSPSLKKLaKQLLGLD-IqegEHSSVEDAR 145
DEDDh_RNase cd06137
DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX) ...
 9-102 2.20e-03

DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins; This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. 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. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA.


Pssm-ID: 99840  Cd Length: 161  Bit Score: 38.03  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   9 IAFDIETTGLDFHQDAVIQISAARYVDGiEVDYfDTLV-NSDYIPDEITKLTGIT----NDQVLNAPTL--DEVMPY-LF 80
Cdd:cd06137    1 VALDCEMVGLADGDSEVVRISAVDVLTG-EVLI-DSLVrPSVRVTDWRTRFSGVTpadlEEAAKAGKTIfgWEAARAaLW 78

                         90       100
                 ....*....|....*....|...
gi 487338750  81 DYL-GDTILVGHNIKSfDFPFLK 102
Cdd:cd06137   79 KFIdPDTILVGHSLQN-DLDALR 100
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 196-237 2.53e-03

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


Pssm-ID: 349339 [Multi-domain]  Cd Length: 68  Bit Score: 35.80  E-value: 2.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 487338750 196 MSFVVTGafdDSKYNRKQIETLIKQHGGRVSSSLSAKTDYFI 237
Cdd:cd00027    1 LVICFSG---LDDEEREELKKLIEALGGKVSESLSSKVTHLI 39
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 7-117 3.38e-03

DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 38.88  E-value: 3.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 487338750   7 EFIAFDIETTGLDFHQDAVIQISAArYVDGIEVdyfdtlvnsdYIPDEITKLTGITNDQVLNAptldeVMPYLFDylgDT 86
Cdd:COG0749    2 GLVAFDTETTSLDPMDAELVGISFA-VEPGEAA----------YIPLAHGAPEQLDLDEVLAA-----LKPLLED---PA 62

                         90       100       110
                 ....*....|....*....|....*....|..
gi 487338750  87 IL-VGHNIKsFDFPFLKAKGYNIAegHEIYDT 117
Cdd:COG0749   63 IPkIGQNLK-YDLHVLARYGIELA--GVAFDT 91
 
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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