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Conserved domains on  [gi|1735216163|gb|KAA0057957|]
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protein NEN1 [Cucumis melo var. makuwa]

Protein Classification

3'-5' exonuclease( domain architecture ID 10149829)

3'-5' exonuclease similar to DNA polymerase III subunit epsilon and exodeoxyribonuclease 10

Gene Ontology:  GO:0008408|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-174 1.38e-21

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: 91.21  E-value: 1.38e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  11 AFFDVETT-VPTRQGQkfsILEFGAILVCPKKLVElESYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVY 89
Cdd:cd06127     1 VVFDTETTgLDPKKDR---IIEIGAVKVDGGIEIV-ERFETLVNPGRPIPPEATAI--HGITDEMLADAPPFEEVLPEFL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  90 DILHGRIWAGHNIlRFDCARIREAFADIGVPaPEPKGTIDSLALLTQRFGRRAGDMKVMTEFSLLHANSGD--QSLDDVR 167
Cdd:cd06127    75 EFLGGRVLVAHNA-SFDLRFLNRELRRLGGP-PLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGahRALADAL 152


                  ....*..
gi 1735216163 168 MNLEVLK 174
Cdd:cd06127   153 ATAELLL 159
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-174 1.38e-21

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: 91.21  E-value: 1.38e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  11 AFFDVETT-VPTRQGQkfsILEFGAILVCPKKLVElESYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVY 89
Cdd:cd06127     1 VVFDTETTgLDPKKDR---IIEIGAVKVDGGIEIV-ERFETLVNPGRPIPPEATAI--HGITDEMLADAPPFEEVLPEFL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  90 DILHGRIWAGHNIlRFDCARIREAFADIGVPaPEPKGTIDSLALLTQRFGRRAGDMKVMTEFSLLHANSGD--QSLDDVR 167
Cdd:cd06127    75 EFLGGRVLVAHNA-SFDLRFLNRELRRLGGP-PLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGahRALADAL 152


                  ....*..
gi 1735216163 168 MNLEVLK 174
Cdd:cd06127   153 ATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 12-181 4.59e-21

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.05  E-value: 4.59e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   12 FFDVETTVptRQGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDI 91
Cdd:smart00479   4 VIDCETTG--LDPGKDEIIEIAAVDVDGGEIIE--VFDTYVKPDRPITDYATEI--HGITPEMLDDAPTFEEVLEELLEF 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   92 LHGRIWAGHNILRFDCARIREAFADIGVPAPEPKGTIDSLALLTQRFGRRAGD-MKVMTEfSLLHANSGDQ--SLDDVRM 168
Cdd:smart00479  78 LRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYsLKKLAK-RLLLEVIQRAhrALDDARA 156

                          170
                   ....*....|...
gi 1735216163  169 NLEVLKYCATVLF 181
Cdd:smart00479 157 TAKLFKKLLERLE 169
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 9-138 8.27e-18

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 80.61  E-value: 8.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   9 EIAFFDVETTvpTRQGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRV 88
Cdd:COG0847     1 RFVVLDTETT--GLDPAKDRIIEIGAVKVDDGRIVE--TFHTLVNPERPIPPEATAI--HGITDEDVADAPPFAEVLPEL 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1735216163  89 YDILHGRIWAGHNIlRFDCARIREAFADIGVPAPEPKgTIDSLALLTQRF 138
Cdd:COG0847    75 LEFLGGAVLVAHNA-AFDLGFLNAELRRAGLPLPPFP-VLDTLRLARRLL 122
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 12-173 9.43e-17

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: 77.78  E-value: 9.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  12 FFDVETTVPtrQGQKFSILEFGAILVCPKKLVELESYSTLVKPSDLSLISSLSVRCNGITRDAVISSPTFAQIADRVYDI 91
Cdd:pfam00929   2 VIDLETTGL--DPEKDEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  92 L-HGRIWAGHNIlRFDCARIREAFADIG-VPAPEPKGTIDSLALLTQRFGRRAG--DMKVMTEFSLLHANSGDQSLDDVR 167
Cdd:pfam00929  80 LrKGNLLVAHNA-SFDVGFLRYDDKRFLkKPMPKLNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIGRAHRALDDAR 158


                  ....*.
gi 1735216163 168 MNLEVL 173
Cdd:pfam00929 159 ATAKLF 164
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 14-133 7.43e-06

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 48.79  E-value: 7.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  14 DVETT--VPtRQGQKfsILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDI 91
Cdd:PRK08074    9 DLETTgnSP-KKGDK--IIQIAAVVVEDGEILE--RFSSFVNPERPIPPFITEL--TGISEEMVKQAPLFEDVAPEIVEL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1735216163  92 LHGRIWAGHNIlRFDCARIREAFADIGVPAPEPKgTIDSLAL 133
Cdd:PRK08074   82 LEGAYFVAHNV-HFDLNFLNEELERAGYTEIHCP-KLDTVEL 121
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 13-114 4.86e-04

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: 41.67  E-value: 4.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  13 FDVETTVPTrqgQKFSILEFGAILVCPKKLVELESYsTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDIL 92
Cdd:TIGR00573  12 GDNETTGLY---AGHDIIEIGAVEIINRRITGNKFH-TYIKPDRPIDPDAIKI--HGITDDMLKDKPDFKEIAEDFADYI 85

                          90       100
                  ....*....|....*....|..
gi 1735216163  93 HGRIWAGHNIlRFDCARIREAF 114
Cdd:TIGR00573  86 RGAELVIHNA-SFDVGFLNYEF 106
 
Name Accession Description Interval E-value
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 11-174 1.38e-21

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: 91.21  E-value: 1.38e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  11 AFFDVETT-VPTRQGQkfsILEFGAILVCPKKLVElESYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVY 89
Cdd:cd06127     1 VVFDTETTgLDPKKDR---IIEIGAVKVDGGIEIV-ERFETLVNPGRPIPPEATAI--HGITDEMLADAPPFEEVLPEFL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  90 DILHGRIWAGHNIlRFDCARIREAFADIGVPaPEPKGTIDSLALLTQRFGRRAGDMKVMTEFSLLHANSGD--QSLDDVR 167
Cdd:cd06127    75 EFLGGRVLVAHNA-SFDLRFLNRELRRLGGP-PLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGahRALADAL 152


                  ....*..
gi 1735216163 168 MNLEVLK 174
Cdd:cd06127   153 ATAELLL 159
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 12-181 4.59e-21

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 90.05  E-value: 4.59e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   12 FFDVETTVptRQGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDI 91
Cdd:smart00479   4 VIDCETTG--LDPGKDEIIEIAAVDVDGGEIIE--VFDTYVKPDRPITDYATEI--HGITPEMLDDAPTFEEVLEELLEF 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   92 LHGRIWAGHNILRFDCARIREAFADIGVPAPEPKGTIDSLALLTQRFGRRAGD-MKVMTEfSLLHANSGDQ--SLDDVRM 168
Cdd:smart00479  78 LRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYsLKKLAK-RLLLEVIQRAhrALDDARA 156

                          170
                   ....*....|...
gi 1735216163  169 NLEVLKYCATVLF 181
Cdd:smart00479 157 TAKLFKKLLERLE 169
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 9-138 8.27e-18

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 80.61  E-value: 8.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   9 EIAFFDVETTvpTRQGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRV 88
Cdd:COG0847     1 RFVVLDTETT--GLDPAKDRIIEIGAVKVDDGRIVE--TFHTLVNPERPIPPEATAI--HGITDEDVADAPPFAEVLPEL 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1735216163  89 YDILHGRIWAGHNIlRFDCARIREAFADIGVPAPEPKgTIDSLALLTQRF 138
Cdd:COG0847    75 LEFLGGAVLVAHNA-AFDLGFLNAELRRAGLPLPPFP-VLDTLRLARRLL 122
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 1-133 8.65e-17

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 78.26  E-value: 8.65e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   1 MGPTEDRSEIAFFDVETTvptrqG---QKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSlsVRCNGITRDAVIS 77
Cdd:COG2176     1 MSLDLEDLTYVVFDLETT-----GlspKKDEIIEIGAVKVENGEIVD--RFSTLVNPGRPIPPFI--TELTGITDEMVAD 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1735216163  78 SPTFAQIADRVYDILHGRIWAGHNIlRFDCARIREAFADIGVPAPEPkgTIDSLAL 133
Cdd:COG2176    72 APPFEEVLPEFLEFLGDAVLVAHNA-SFDLGFLNAALKRLGLPFDNP--VLDTLEL 124
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 12-173 9.43e-17

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: 77.78  E-value: 9.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  12 FFDVETTVPtrQGQKFSILEFGAILVCPKKLVELESYSTLVKPSDLSLISSLSVRCNGITRDAVISSPTFAQIADRVYDI 91
Cdd:pfam00929   2 VIDLETTGL--DPEKDEIIEIAAVVIDGGENEIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEF 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  92 L-HGRIWAGHNIlRFDCARIREAFADIG-VPAPEPKGTIDSLALLTQRFGRRAG--DMKVMTEFSLLHANSGDQSLDDVR 167
Cdd:pfam00929  80 LrKGNLLVAHNA-SFDVGFLRYDDKRFLkKPMPKLNPVIDTLILDKATYKELPGrsLDALAEKLGLEHIGRAHRALDDAR 158


                  ....*.
gi 1735216163 168 MNLEVL 173
Cdd:pfam00929 159 ATAKLF 164
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 13-123 2.25e-10

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: 59.06  E-value: 2.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  13 FDVETTvptrQGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSlsVRCNGITRDAVISSPTFAQIADRVYDIL 92
Cdd:cd06130     4 IDFETA----NADRASACSIGLVKVRDGQIVD--TFYTLIRPPTRFDPFN--IAIHGITPEDVADAPTFPEVWPEIKPFL 75

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1735216163  93 HGRIWAGHNIlRFDCARIREAFADIGVPAPE 123
Cdd:cd06130    76 GGSLVVAHNA-SFDRSVLRAALEAYGLPPPP 105
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 12-142 3.12e-06

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: 47.14  E-value: 3.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  12 FFDVETT-VPTRQGQKfsILEFGAILVCPKKLVElESYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYD 90
Cdd:cd06131     3 VLDTETTgLDPREGHR--IIEIGCVELINRRLTG-NTFHVYINPERDIPEEAFKV--HGITDEFLADKPKFAEIADEFLD 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1735216163  91 ILHGRIWAGHNiLRFDCARI-REAFADIGVPAPEPKGT-IDSLALLTQRF-GRRA 142
Cdd:cd06131    78 FIRGAELVIHN-ASFDVGFLnAELSLLGLGKKIIDFCRvIDTLALARKKFpGKPN 131
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 14-133 7.43e-06

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 48.79  E-value: 7.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  14 DVETT--VPtRQGQKfsILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDI 91
Cdd:PRK08074    9 DLETTgnSP-KKGDK--IIQIAAVVVEDGEILE--RFSSFVNPERPIPPFITEL--TGISEEMVKQAPLFEDVAPEIVEL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1735216163  92 LHGRIWAGHNIlRFDCARIREAFADIGVPAPEPKgTIDSLAL 133
Cdd:PRK08074   82 LEGAYFVAHNV-HFDLNFLNEELERAGYTEIHCP-KLDTVEL 121
PRK06063 PRK06063
DEDDh family exonuclease;
2-174 8.03e-06

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 47.77  E-value: 8.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   2 GPTEDRSEIAFFDVETTvPTRQGQKfSILEFGAILVCPKKLVElESYSTLVKPSDLSLIsslsVRCNGITRDAVISSPTF 81
Cdd:PRK06063    9 PASHYPRGWAVVDVETS-GFRPGQA-RIISLAVLGLDADGNVE-QSVVTLLNPGVDPGP----THVHGLTAEMLEGQPQF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  82 AQIADRVYDILHGRIWAGHNILrFDCARIREAFADIGVPAPepkgtIDSlALLTQRFGRRAG----DMKVMTefslLHAN 157
Cdd:PRK06063   82 ADIAGEVAELLRGRTLVAHNVA-FDYSFLAAEAERAGAELP-----VDQ-VMCTVELARRLGlglpNLRLET----LAAH 150

                         170       180
                  ....*....|....*....|...
gi 1735216163 158 SG------DQSLDDVRMNLEVLK 174
Cdd:PRK06063  151 WGvpqqrpHDALDDARVLAGILR 173
polC PRK00448
DNA polymerase III PolC; Validated
 13-133 6.61e-05

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 45.98  E-value: 6.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   13 FDVETTvptrqGqkFS-----ILEFGAILVcpKKLVELESYSTLVKPSDLSLISSlsVRCNGITRDAVISSPTFAQIADR 87
Cdd:PRK00448   424 FDVETT-----G--LSavydeIIEIGAVKI--KNGEIIDKFEFFIKPGHPLSAFT--TELTGITDDMVKDAPSIEEVLPK 492

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1735216163   88 VYDILHGRIWAGHNIlRFDCARIREAFADIGVPAPEPkGTIDSLAL 133
Cdd:PRK00448   493 FKEFCGDSILVAHNA-SFDVGFINTNYEKLGLEKIKN-PVIDTLEL 536
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
8-133 3.34e-04

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 43.37  E-value: 3.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163   8 SEIAF--FDVETTVPTRQGQkfSILEFGAILVCPKklVELESYSTLVKPSDLSLISSlsVRCNGITRDAVISSPTFAQIA 85
Cdd:PRK07883   13 RDVTFvvVDLETTGGSPAGD--AITEIGAVKVRGG--EVLGEFATLVNPGRPIPPFI--TVLTGITTAMVAGAPPIEEVL 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1735216163  86 DRVYDILHGRIWAGHNiLRFDCARIREAFADIGVPAPEPKgTIDSLAL 133
Cdd:PRK07883   87 PAFLEFARGAVLVAHN-APFDIGFLRAAAARCGYPWPGPP-VLCTVRL 132
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 13-114 4.86e-04

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: 41.67  E-value: 4.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  13 FDVETTVPTrqgQKFSILEFGAILVCPKKLVELESYsTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDIL 92
Cdd:TIGR00573  12 GDNETTGLY---AGHDIIEIGAVEIINRRITGNKFH-TYIKPDRPIDPDAIKI--HGITDDMLKDKPDFKEIAEDFADYI 85

                          90       100
                  ....*....|....*....|..
gi 1735216163  93 HGRIWAGHNIlRFDCARIREAF 114
Cdd:TIGR00573  86 RGAELVIHNA-SFDVGFLNYEF 106
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 12-96 1.60e-03

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 39.51  E-value: 1.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  12 FFDVETTVP---TRQGQKFSILEFGAILVCPKKLVELESYSTLVKPSDLSLISSLSVRCNGITRDAVISSPTFAQIADRV 88
Cdd:cd06133     3 VIDFEATCWegnSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEF 82


                  ....*...
gi 1735216163  89 YDILHGRI 96
Cdd:cd06133    83 LEWLGKNG 90
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 12-131 3.88e-03

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 39.02  E-value: 3.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  12 FFDVETTvpTRQGQKFSILEFGAIlvcpkKLVELESYSTLVKPSDLSLISSLSVrcNGITRDAVISSPTFAQIADRVYDI 91
Cdd:PRK06309    6 FYDTETT--GTQIDKDRIIEIAAY-----NGVTSESFQTLVNPEIPIPAEASKI--HGITTDEVADAPKFPEAYQKFIEF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1735216163  92 LHGR-IWAGHNILRFDCARIREAFADIGVPAPEPKgTIDSL 131
Cdd:PRK06309   77 CGTDnILVAHNNDAFDFPLLRKECRRHGLEPPTLR-TIDSL 116
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 11-113 4.86e-03

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 39.67  E-value: 4.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  11 AFFDVETTVPtrqGQKFSILEFGAILVCPKKLVEleSYSTLVKPSDLSLISSlsVRCNGITRDAVISSPTFAQIADRVYD 90
Cdd:PRK07246   10 AVVDLEATGA---GPNASIIQVGIVIIEGGEIID--SYTTDVNPHEPLDEHI--KHLTGITDQQLAQAPDFSQVARHIYD 82

                          90       100
                  ....*....|....*....|...
gi 1735216163  91 ILHGRIWAGHNIlRFDCARIREA 113
Cdd:PRK07246   83 LIEDCIFVAHNV-KFDANLLAEA 104
ExoI_N cd06138
N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar ...
 11-114 6.90e-03

N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease 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. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.


Pssm-ID: 99841 [Multi-domain]  Cd Length: 183  Bit Score: 37.63  E-value: 6.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735216163  11 AFFDVETT--VPTRQgqkfSILEFGAILVcPKKLVELESYSTLVKPSDLSLISSLSVRCNGITRDAVISS-PTFAQIADR 87
Cdd:cd06138     1 LFYDYETFglNPSFD----QILQFAAIRT-DENFNEIEPFNIFCRLPPDVLPSPEALIVTGITPQQLLKEgLSEYEFIAK 75

                          90       100
                  ....*....|....*....|....*....
gi 1735216163  88 VYDILH--GRIWAGHNILRFDCARIREAF 114
Cdd:cd06138    76 IHRLFNtpGTCIVGYNNIRFDDEFLRFAF 104
 
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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