NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|499975509|ref|WP_011656227|]
View 

exonuclease domain-containing protein [Burkholderia ambifaria]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 12-182 2.09e-69

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


:

Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 215.78  E-value: 2.09e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTL 86
Cdd:COG2176    7 DLTYVVFDLETTGLSPKKDEIIEIGAVkvengEI----VDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  87 FERLDGKLFVAHNASFDRGFLRAEFERAGIAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADADLLW 166
Cdd:COG2176   83 LEFLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATA 162

                        170
                 ....*....|....*....
gi 499975509 167 QFWRQLHEIV---PLERLR 182
Cdd:COG2176  163 ELFLKLLEKLeekGITTLR 181
GIY-YIG_UvrC_Cho cd10434
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ...
 206-286 4.08e-27

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.


:

Pssm-ID: 198381 [Multi-domain]  Cd Length: 81  Bit Score: 102.56  E-value: 4.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 206 APAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRPSHN 285
Cdd:cd10434    1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYN 80


                 .
gi 499975509 286 R 286
Cdd:cd10434   81 I 81
 
Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 12-182 2.09e-69

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 215.78  E-value: 2.09e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTL 86
Cdd:COG2176    7 DLTYVVFDLETTGLSPKKDEIIEIGAVkvengEI----VDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  87 FERLDGKLFVAHNASFDRGFLRAEFERAGIAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADADLLW 166
Cdd:COG2176   83 LEFLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATA 162

                        170
                 ....*....|....*....
gi 499975509 167 QFWRQLHEIV---PLERLR 182
Cdd:COG2176  163 ELFLKLLEKLeekGITTLR 181
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
12-287 6.15e-67

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 220.95  E-value: 6.15e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK07883  14 DVTFVVVDLETTGGSPAGDAITEIGAVKVrGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  91 DGKLFVAHNASFDRGFLRAEFERAGIAF-NPDVLCTVRLSRALFPREA--RHGLDALIERHGLVPAARHRALADA----D 163
Cdd:PRK07883  94 RGAVLVAHNAPFDIGFLRAAAARCGYPWpGPPVLCTVRLARRVLPRDEapNVRLSTLARLFGATTTPTHRALDDAratvD 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 164 LLWQFWRQL--HEIVPLERLRDQIARTTRHFRlaggMTEAWLDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTG 241
Cdd:PRK07883 174 VLHGLIERLgnLGVHTLEELLTYLPRVTPAQR----RKRHLADGLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTA 249

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 499975509 242 --ERRSSKEMrlAQQVRRVEWRETGNELGAMLAEAQWIARLRPSHNRR 287
Cdd:PRK07883 250 aeTRGRMREM--VALAERVDHVECAHALEAEVRELRLIAAHKPPYNRR 295
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 16-162 5.59e-52

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: 170.17  E-value: 5.59e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGSSAEHRITEIGVVEI--GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVdgGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499975509  94 LFVAHNASFDRGFLRAEFERAG-IAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPA-ARHRALADA 162
Cdd:cd06127   81 VLVAHNASFDLRFLNRELRRLGgPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLeGAHRALADA 151
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 16-192 4.35e-42

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


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 156.89  E-value: 4.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   16 VFVDLETTGGSSAEHRITEIG--VVEIGPLgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:TIGR01407   3 AVVDLETTGTQLSFDKIIQIGivVVEDGEI-VDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   94 LFVAHNASFDRGFLRAEFERAGIAFNPD-VLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADAD-------LL 165
Cdd:TIGR01407  82 IFVAHNVHFDLNFLAKALKDCGYEPLPKpRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQataelllLL 161

                         170       180
                  ....*....|....*....|....*....
gi 499975509  166 WQFWRQLHEIV--PLERLRDQIARTTRHF 192
Cdd:TIGR01407 162 FEKMEKLPLDTleQLLELSDQLLYESYDI 190
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 15-162 1.06e-41

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 143.98  E-value: 1.06e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509    15 LVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509    94 LFVAHN-ASFDRGFLRAEFERAGIAFNPD--VLCTVRLSRALFPREARHGLDALIERHGL-VPAARHRALADA 162
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKlpVIDTLKLARATNPGLPKYSLKKLAKRLLLeVIQRAHRALDDA 154
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 16-162 4.45e-34

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: 123.62  E-value: 4.45e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   16 VFVDLETTGGSSAEHRITEIGVVEI---GPLGVSTWTTLVNPGQS--IPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIdggENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499975509   91 D-GKLFVAHNASFDRGFLRAEFERAG---IAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAAR-HRALADA 162
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLkkpMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDA 157
GIY-YIG_UvrC_Cho cd10434
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ...
 206-286 4.08e-27

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.


Pssm-ID: 198381 [Multi-domain]  Cd Length: 81  Bit Score: 102.56  E-value: 4.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 206 APAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRPSHN 285
Cdd:cd10434    1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYN 80


                 .
gi 499975509 286 R 286
Cdd:cd10434   81 I 81
PRK10545 PRK10545
excinuclease Cho;
201-338 1.21e-17

excinuclease Cho;


Pssm-ID: 182535  Cd Length: 286  Bit Score: 82.03  E-value: 1.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 201 AWLDTAPAGCGVYALFGEGDE-ALYVGRSVRVRQRLRALLtgerRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIAR 279
Cdd:PRK10545  26 PFLEDLPKLPGVYLFHGESDTmPLYIGKSVNIRSRVLSHL----RTPDEAAMLRQSRRISWICTAGEIGALLLEARLIKE 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 280 LRP--------------------------------SH---------NRRPA-------AD------------KARAGNA- 298
Cdd:PRK10545 102 QQPlfnkrlrrnrqlcslqlnegrvdvvyakevdfSRapnlfglfaNRRAAlqalqsiADeqklcygllglePLSRGRAc 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499975509 299 -----------------------------------GWPFDGAVAF-EAGDERRLFHVIDGWRYLGAAESLDAAMRL 338
Cdd:PRK10545 182 frsalkrcagaccgkesheahalrlraslerlrvvCWPWQGAVALkEQGPEMTQYHIIQNWLWLGAVNSLEEAATL 257
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
203-282 7.84e-10

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 60.14  E-value: 7.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 203 LDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:COG0322   10 LKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNLIKKHKP 89
uvrC TIGR00194
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ...
 203-302 6.11e-08

excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272953 [Multi-domain]  Cd Length: 574  Bit Score: 54.30  E-value: 6.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  203 LDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTgERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:TIGR00194   5 LKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFR-ENNSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQP 83

                          90       100
                  ....*....|....*....|
gi 499975509  283 SHNRRPAADKaragnaGWPF 302
Cdd:TIGR00194  84 RYNVLLKDDK------GYPY 97
GIYc smart00465
GIY-YIG type nucleases (URI domain);
211-287 1.54e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 40.10  E-value: 1.54e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499975509   211 GVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSK-EMRLAQQVRRVEWRETGNELGAML-AEAQWIARLRPSHNRR 287
Cdd:smart00465   3 GVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLlIDALLKYGGNFEFIILESFDESALeLEKYLIKEYKPKYNLL 81
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 210-282 2.13e-03

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 36.55  E-value: 2.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509  210 CGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:pfam01541   2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRP 74
 
Name Accession Description Interval E-value
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 12-182 2.09e-69

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


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 215.78  E-value: 2.09e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTL 86
Cdd:COG2176    7 DLTYVVFDLETTGLSPKKDEIIEIGAVkvengEI----VDRFSTLVNPGRPIPPFITELTGITDEMVADAPPFEEVLPEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  87 FERLDGKLFVAHNASFDRGFLRAEFERAGIAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADADLLW 166
Cdd:COG2176   83 LEFLGDAVLVAHNASFDLGFLNAALKRLGLPFDNPVLDTLELARRLLPELKSYKLDTLAERLGIPLEDRHRALGDAEATA 162

                        170
                 ....*....|....*....
gi 499975509 167 QFWRQLHEIV---PLERLR 182
Cdd:COG2176  163 ELFLKLLEKLeekGITTLR 181
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
12-287 6.15e-67

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 220.95  E-value: 6.15e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK07883  14 DVTFVVVDLETTGGSPAGDAITEIGAVKVrGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLEFA 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  91 DGKLFVAHNASFDRGFLRAEFERAGIAF-NPDVLCTVRLSRALFPREA--RHGLDALIERHGLVPAARHRALADA----D 163
Cdd:PRK07883  94 RGAVLVAHNAPFDIGFLRAAAARCGYPWpGPPVLCTVRLARRVLPRDEapNVRLSTLARLFGATTTPTHRALDDAratvD 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 164 LLWQFWRQL--HEIVPLERLRDQIARTTRHFRlaggMTEAWLDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTG 241
Cdd:PRK07883 174 VLHGLIERLgnLGVHTLEELLTYLPRVTPAQR----RKRHLADGLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTA 249

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 499975509 242 --ERRSSKEMrlAQQVRRVEWRETGNELGAMLAEAQWIARLRPSHNRR 287
Cdd:PRK07883 250 aeTRGRMREM--VALAERVDHVECAHALEAEVRELRLIAAHKPPYNRR 295
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 14-174 5.78e-61

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 193.47  E-value: 5.78e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  14 PLVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDG 92
Cdd:COG0847    1 RFVVLDTETTGLDPAKDRIIEIGAVKVdDGRIVETFHTLVNPERPIPPEATAIHGITDEDVADAPPFAEVLPELLEFLGG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  93 KLFVAHNASFDRGFLRAEFERAGIAFNP-DVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADADLLWQFWRQ 171
Cdd:COG0847   81 AVLVAHNAAFDLGFLNAELRRAGLPLPPfPVLDTLRLARRLLPGLPSYSLDALCERLGIPFDERHRALADAEATAELFLA 160


                 ...
gi 499975509 172 LHE 174
Cdd:COG0847  161 LLR 163
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 16-162 5.59e-52

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: 170.17  E-value: 5.59e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGSSAEHRITEIGVVEI--GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:cd06127    1 VVFDTETTGLDPKKDRIIEIGAVKVdgGIEIVERFETLVNPGRPIPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499975509  94 LFVAHNASFDRGFLRAEFERAG-IAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPA-ARHRALADA 162
Cdd:cd06127   81 VLVAHNASFDLRFLNRELRRLGgPPLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLeGAHRALADA 151
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 16-193 1.66e-48

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 175.53  E-value: 1.66e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGS-SAEHRITEIG--VVEIGPLgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDG 92
Cdd:PRK08074   6 VVVDLETTGNSpKKGDKIIQIAavVVEDGEI-LERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIVELLEG 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  93 KLFVAHNASFDRGFLRAEFERAGIAFnPDVLC--TVRLSRALFPREARHGLDALIERHGLVPAARHRALADA----DLLW 166
Cdd:PRK08074  85 AYFVAHNVHFDLNFLNEELERAGYTE-IHCPKldTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAevtaELFL 163

                        170       180
                 ....*....|....*....|....*....
gi 499975509 167 QFwrqLHEI--VPLERLRdQIARTTRHFR 193
Cdd:PRK08074 164 QL---LNKLerLPLVTLQ-QLRRLSDHLK 188
dinG_rel TIGR01407
DnaQ family exonuclease/DinG family helicase, putative; This model represents a family of ...
 16-192 4.35e-42

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


Pssm-ID: 273602 [Multi-domain]  Cd Length: 850  Bit Score: 156.89  E-value: 4.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   16 VFVDLETTGGSSAEHRITEIG--VVEIGPLgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:TIGR01407   3 AVVDLETTGTQLSFDKIIQIGivVVEDGEI-VDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYDLLEDG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   94 LFVAHNASFDRGFLRAEFERAGIAFNPD-VLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADAD-------LL 165
Cdd:TIGR01407  82 IFVAHNVHFDLNFLAKALKDCGYEPLPKpRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQataelllLL 161

                         170       180
                  ....*....|....*....|....*....
gi 499975509  166 WQFWRQLHEIV--PLERLRDQIARTTRHF 192
Cdd:TIGR01407 162 FEKMEKLPLDTleQLLELSDQLLYESYDI 190
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 15-162 1.06e-41

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 143.98  E-value: 1.06e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509    15 LVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:smart00479   2 LVVIDCETTGLDPGKDEIIEIAAVDVdGGEIIEVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGR 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509    94 LFVAHN-ASFDRGFLRAEFERAGIAFNPD--VLCTVRLSRALFPREARHGLDALIERHGL-VPAARHRALADA 162
Cdd:smart00479  82 ILVAGNsAHFDLRFLKLEHPRLGIKQPPKlpVIDTLKLARATNPGLPKYSLKKLAKRLLLeVIQRAHRALDDA 154
polC PRK00448
DNA polymerase III PolC; Validated
 16-175 5.69e-38

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 145.37  E-value: 5.69e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   16 VFvDLETTGGSSAEHRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK00448  423 VF-DVETTGLSAVYDEIIEIGAVkikngEI----IDKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFC 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   91 DGKLFVAHNASFDRGFLRAEFERAGIAF--NPdVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADA----DL 164
Cdd:PRK00448  498 GDSILVAHNASFDVGFINTNYEKLGLEKikNP-VIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAeataYL 576

                         170
                  ....*....|.
gi 499975509  165 LWQFWRQLHEI 175
Cdd:PRK00448  577 LIKFLKDLKEK 587
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 16-162 4.45e-34

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: 123.62  E-value: 4.45e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   16 VFVDLETTGGSSAEHRITEIGVVEI---GPLGVSTWTTLVNPGQS--IPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:pfam00929   1 VVIDLETTGLDPEKDEIIEIAAVVIdggENEIGETFHTYVKPTRLpkLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499975509   91 D-GKLFVAHNASFDRGFLRAEFERAG---IAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAAR-HRALADA 162
Cdd:pfam00929  81 RkGNLLVAHNASFDVGFLRYDDKRFLkkpMPKLNPVIDTLILDKATYKELPGRSLDALAEKLGLEHIGRaHRALDDA 157
DNA_pol_III_epsilon_Ecoli_like cd06131
DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III ...
 15-165 1.09e-32

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: 120.33  E-value: 1.09e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  15 LVFVDLETTGGSSAE-HRITEIGVVEI--GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLD 91
Cdd:cd06131    1 QIVLDTETTGLDPREgHRIIEIGCVELinRRLTGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDFIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  92 GKLFVAHNASFDRGFLRAEFERAGIAFNPD----VLCTVRLSRALFPReARHGLDALIERHGLVPAAR--HRALADADLL 165
Cdd:cd06131   81 GAELVIHNASFDVGFLNAELSLLGLGKKIIdfcrVIDTLALARKKFPG-KPNSLDALCKRFGIDNSHRtlHGALLDAELL 159
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 16-162 1.94e-32

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: 119.15  E-value: 1.94e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGSSAehRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:cd06130    2 VAIDFETANADRA--SACSIGLVkvrdgQI----VDTFYTLIRPPTRFDPFNIAIHGITPEDVADAPTFPEVWPEIKPFL 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509  91 DGKLFVAHNASFDRGFLRAEFERAGIAF-NPDVLCTVRLSRALFPREARHGLDALIERHGLvPAARHRALADA 162
Cdd:cd06130   76 GGSLVVAHNASFDRSVLRAALEAYGLPPpPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGI-ELNHHDALEDA 147
PRK08517 PRK08517
3'-5' exonuclease;
12-162 2.89e-30

3'-5' exonuclease;


Pssm-ID: 236281 [Multi-domain]  Cd Length: 257  Bit Score: 116.27  E-value: 2.89e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNpGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK08517  67 DQVFCFVDIETNGSKPKKHQIIEIGAVKVkNGEIIDRFESFVK-AKEVPEYITELTGITYEDLENAPSLKEVLEEFRLFL 145

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499975509  91 DGKLFVAHNASFDRGFLRAEFERAG--IAFNPDvLCTVRLSRALFPREaRHGLDALIERHGLVPAARHRALADA 162
Cdd:PRK08517 146 GDSVFVAHNVNFDYNFISRSLEEIGlgPLLNRK-LCTIDLAKRTIESP-RYGLSFLKELLGIEIEVHHRAYADA 217
GIY-YIG_UvrC_Cho cd10434
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ...
 206-286 4.08e-27

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.


Pssm-ID: 198381 [Multi-domain]  Cd Length: 81  Bit Score: 102.56  E-value: 4.08e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 206 APAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRPSHN 285
Cdd:cd10434    1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYFTGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRYN 80


                 .
gi 499975509 286 R 286
Cdd:cd10434   81 I 81
dnaq TIGR00573
exonuclease, DNA polymerase III, epsilon subunit family; All proteins in this family for which ...
 19-167 1.30e-25

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: 102.91  E-value: 1.30e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   19 DLETTGgSSAEHRITEIGVVEI--GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGKLFV 96
Cdd:TIGR00573  13 DNETTG-LYAGHDIIEIGAVEIinRRITGNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAEDFADYIRGAELV 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499975509   97 AHNASFDRGFLRAEFER---AGIAFNP--DVLCTVRLSRALFPREaRHGLDALIERHGLV--PAARHRALADADLLWQ 167
Cdd:TIGR00573  92 IHNASFDVGFLNYEFSKlykVEPKTNDviDTTDTLQYARPEFPGK-RNTLDALCKRYEITnsHRALHGALADAFILAK 168
PRK07740 PRK07740
hypothetical protein; Provisional
 8-172 9.72e-25

hypothetical protein; Provisional


Pssm-ID: 236085 [Multi-domain]  Cd Length: 244  Bit Score: 101.28  E-value: 9.72e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   8 DPACEQPLVFVDLETTGGS-SAEHRITEIGVVEI--GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAP 84
Cdd:PRK07740  54 IPLTDLPFVVFDLETTGFSpQQGDEILSIGAVKTkgGEVETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLH 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  85 TLFERLDGKLFVAHNASFDRGFLRAEFERA-GIAFNPDVLCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADAD 163
Cdd:PRK07740 134 RFYAFIGAGVLVAHHAGHDKAFLRHALWRTyRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDAL 213


                 ....*....
gi 499975509 164 LLWQFWRQL 172
Cdd:PRK07740 214 MTAKLWAIL 222
PRK05711 PRK05711
DNA polymerase III subunit epsilon; Provisional
 19-165 1.84e-24

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 235574 [Multi-domain]  Cd Length: 240  Bit Score: 100.32  E-value: 1.84e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  19 DLETTG-GSSAEHRITEIGVVEI---GPLGvSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGKL 94
Cdd:PRK05711  10 DTETTGlNQREGHRIIEIGAVELinrRLTG-RNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEFLDFIRGAE 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499975509  95 FVAHNASFDRGFLRAEFERAGIAFNP-----DVLCTVRLSRALFPrEARHGLDALIERHGLVPAAR--HRALADADLL 165
Cdd:PRK05711  89 LIIHNAPFDIGFMDYEFALLGRDIPKtntfcKVTDTLAMARRMFP-GKRNSLDALCKRYGIDNSHRtlHGALLDAEIL 165
PRK06063 PRK06063
DEDDh family exonuclease;
1-170 1.11e-23

DEDDh family exonuclease;


Pssm-ID: 180377 [Multi-domain]  Cd Length: 313  Bit Score: 99.78  E-value: 1.11e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   1 MSDSCPSDPACEQP--LVFVDLETTGGSSAEHRITEIGVVEIGPLG--VSTWTTLVNPGQSIPPfiQQLTGISDDMVRDA 76
Cdd:PRK06063   1 MMSHTWGRPASHYPrgWAVVDVETSGFRPGQARIISLAVLGLDADGnvEQSVVTLLNPGVDPGP--THVHGLTAEMLEGQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  77 PSFASLAPTLFERLDGKLFVAHNASFDRGFLRAEFERAGIAFNPD-VLCTVRLSRALFPREARHGLDALIERHGLVPAAR 155
Cdd:PRK06063  79 PQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDqVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRP 158

                        170
                 ....*....|....*
gi 499975509 156 HRALADADLLWQFWR 170
Cdd:PRK06063 159 HDALDDARVLAGILR 173
PRK06807 PRK06807
3'-5' exonuclease;
16-161 5.45e-23

3'-5' exonuclease;


Pssm-ID: 235864 [Multi-domain]  Cd Length: 313  Bit Score: 97.96  E-value: 5.45e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGSSAEHRITEIGVV-----EIgplgVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK06807  11 VVIDFETTGFNPYNDKIIQVAAVkyrnhEL----VDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLFLAFL 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499975509  91 DGKLFVAHNASFDRGFLRAEFERAGIAF-NPDVLCTVRLSRALFPREARHGLDAlIERHGLVPAARHRALAD 161
Cdd:PRK06807  87 HTNVIVAHNASFDMRFLKSNVNMLGLPEpKNKVIDTVFLAKKYMKHAPNHKLET-LKRMLGIRLSSHNAFDD 157
PRK07246 PRK07246
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 16-162 2.33e-18

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


Pssm-ID: 180905 [Multi-domain]  Cd Length: 820  Bit Score: 86.66  E-value: 2.33e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTG-GSSAEhrITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK 93
Cdd:PRK07246  10 AVVDLEATGaGPNAS--IIQVGIVIIeGGEIIDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVARHIYDLIEDC 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509  94 LFVAHNASFDRGFLrAE---FEraGIAF-NPDVlCTVRLSRALFPREARHGLDALIERHGLVPAARHRALADA 162
Cdd:PRK07246  88 IFVAHNVKFDANLL-AEalfLE--GYELrTPRV-DTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADA 156
PRK10545 PRK10545
excinuclease Cho;
201-338 1.21e-17

excinuclease Cho;


Pssm-ID: 182535  Cd Length: 286  Bit Score: 82.03  E-value: 1.21e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 201 AWLDTAPAGCGVYALFGEGDE-ALYVGRSVRVRQRLRALLtgerRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIAR 279
Cdd:PRK10545  26 PFLEDLPKLPGVYLFHGESDTmPLYIGKSVNIRSRVLSHL----RTPDEAAMLRQSRRISWICTAGEIGALLLEARLIKE 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 280 LRP--------------------------------SH---------NRRPA-------AD------------KARAGNA- 298
Cdd:PRK10545 102 QQPlfnkrlrrnrqlcslqlnegrvdvvyakevdfSRapnlfglfaNRRAAlqalqsiADeqklcygllglePLSRGRAc 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499975509 299 -----------------------------------GWPFDGAVAF-EAGDERRLFHVIDGWRYLGAAESLDAAMRL 338
Cdd:PRK10545 182 frsalkrcagaccgkesheahalrlraslerlrvvCWPWQGAVALkEQGPEMTQYHIIQNWLWLGAVNSLEEAATL 257
PRK06309 PRK06309
DNA polymerase III subunit epsilon; Validated
 15-172 7.51e-16

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180524 [Multi-domain]  Cd Length: 232  Bit Score: 76.00  E-value: 7.51e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  15 LVFVDLETTGGSSAEHRITEIGVVEigPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERLDGK- 93
Cdd:PRK06309   4 LIFYDTETTGTQIDKDRIIEIAAYN--GVTSESFQTLVNPEIPIPAEASKIHGITTDEVADAPKFPEAYQKFIEFCGTDn 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  94 LFVAHNA-SFDRGFLRAEFERAGIAfnPDVLCTV---RLSRALFPREARHGLDALIERHGLVPAARHRALADADLLWQFW 169
Cdd:PRK06309  82 ILVAHNNdAFDFPLLRKECRRHGLE--PPTLRTIdslKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALDDVITLHRVF 159


                 ...
gi 499975509 170 RQL 172
Cdd:PRK06309 160 SAL 162
PRK06310 PRK06310
DNA polymerase III subunit epsilon; Validated
 12-172 3.69e-15

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 180525 [Multi-domain]  Cd Length: 250  Bit Score: 74.48  E-value: 3.69e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVVEI-GPLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPTLFERL 90
Cdd:PRK06310   6 DTEFVCLDCETTGLDVKKDRIIEFAAIRFtFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQIKGFF 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  91 -DGKLFVAHNASFDRGFLRAEFERAGIAFNPD---VLCTVRLSRaLFPREARHGLDALiERHGLVPA-ARHRALADADLL 165
Cdd:PRK06310  86 kEGDYIVGHSVGFDLQVLSQESERIGETFLSKhyyIIDTLRLAK-EYGDSPNNSLEAL-AVHFNVPYdGNHRAMKDVEIN 163


                 ....*..
gi 499975509 166 WQFWRQL 172
Cdd:PRK06310 164 IKVFKHL 170
PRK09182 PRK09182
DNA polymerase III subunit epsilon; Validated
 16-118 1.72e-13

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236397 [Multi-domain]  Cd Length: 294  Bit Score: 70.39  E-value: 1.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  16 VFVDLETTGGSSAEHRITEIGVV--EIGPLG-----VSTWTTLVNPGQSIPPFIQQLTGISDDMVR----DAPSFASLAP 84
Cdd:PRK09182  40 VILDTETTGLDPRKDEIIEIGMVafEYDDDGrigdvLDTFGGLQQPSRPIPPEITRLTGITDEMVAgqtiDPAAVDALIA 119

                         90       100       110
                 ....*....|....*....|....*....|....
gi 499975509  85 tlferlDGKLFVAHNASFDRGFLraefERAGIAF 118
Cdd:PRK09182 120 ------PADLIIAHNAGFDRPFL----ERFSPVF 143
PRK07983 PRK07983
exodeoxyribonuclease X; Provisional
 18-165 5.67e-12

exodeoxyribonuclease X; Provisional


Pssm-ID: 181186 [Multi-domain]  Cd Length: 219  Bit Score: 64.74  E-value: 5.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  18 VDLETTGgssaehriTEIGVVEIGPLGV------STWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSFASLAPtlfERLD 91
Cdd:PRK07983   5 IDTETCG--------LQGGIVEIASVDVidgkivNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIP---HYYG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  92 GKLFVAHNASFDRGFLraeferagiafnPDV----LCTVRLSRALFPrEARHGLDALIERHGL---VPAA--RHRALAD- 161
Cdd:PRK07983  74 SEWYVAHNASFDRRVL------------PEMpgewICTMKLARRLWP-GIKYSNMALYKSRKLnvqTPPGlhHHRALYDc 140


                 ....*..
gi 499975509 162 ---ADLL 165
Cdd:PRK07983 141 yitAALL 147
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 64-162 5.16e-11

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 62.88  E-value: 5.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  64 QLTGISDDMVRDAPSFASLAPTLFERLDGKLFVAHNASFDRGFLRAEFERAGIAFnPDV--LCTVRLSRALFPREARHGL 141
Cdd:PRK06195  52 GIHGIRPHMVEDELEFDKIWEKIKHYFNNNLVIAHNASFDISVLRKTLELYNIPM-PSFeyICTMKLAKNFYSNIDNARL 130

                         90       100
                 ....*....|....*....|....*..
gi 499975509 142 DALIE------RHglvpaarHRALADA 162
Cdd:PRK06195 131 NTVNNflgyefKH-------HDALADA 150
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 15-162 3.25e-10

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: 58.77  E-value: 3.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  15 LVFVDLETTGGSSA-----EHRITEIGVVEigpLGVSTWTTL----------VNPGQSipPFIQQLTGISDDMVRDAPSF 79
Cdd:cd06133    1 YLVIDFEATCWEGNskpdyPNEIIEIGAVL---VDVKTKEIIdtfssyvkpvINPKLS--DFCTELTGITQEDVDNAPSF 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  80 ASLAPTLFERLDGKLFVAhNASF---DRGFLRAEFERAGIAFNPDVLCTVRLSRALFPREARH----GLDALIERHGLVP 152
Cdd:cd06133   76 PEVLKEFLEWLGKNGKYA-FVTWgdwDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLkkrtGLSKALEYLGLEF 154

                        170
                 ....*....|.
gi 499975509 153 AAR-HRALADA 162
Cdd:cd06133  155 EGRhHRGLDDA 165
TREX1_2 cd06136
DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar ...
 15-133 5.65e-10

DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins; Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture.


Pssm-ID: 99839 [Multi-domain]  Cd Length: 177  Bit Score: 58.11  E-value: 5.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  15 LVFVDLETTG-GSSAEHRITEIGVVEIG--------------PLGVSTWTTLVNPGQSIPPFIQQLTGISDDMVRDAPSF 79
Cdd:cd06136    1 FVFLDLETTGlPKHNRPEITELCLVAVHrdhllntsrdkpalPRVLDKLSLCFNPGRAISPGASEITGLSNDLLEHKAPF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499975509  80 ----ASLAPTLFERLDGKL-FVAHNAS-FDRGFLRAEFERAGIAFNPDVLC--TVRLSRALF 133
Cdd:cd06136   81 dsdtANLIKLFLRRQPKPIcLVAHNGNrFDFPILRSELERLGTKLPDDILCvdSLPAFRELD 142
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
203-282 7.84e-10

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 60.14  E-value: 7.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 203 LDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:COG0322   10 LKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYFQKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNLIKKHKP 89
PRK07942 PRK07942
DNA polymerase III subunit epsilon; Provisional
 12-185 2.84e-09

DNA polymerase III subunit epsilon; Provisional


Pssm-ID: 181176 [Multi-domain]  Cd Length: 232  Bit Score: 56.91  E-value: 2.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  12 EQPLVFVDLETTGGSSAEHRITEIGVVEIGPLG--VSTWTTLVNPGQSIPPFIQQLTGISDDMVRD-----APSFASLAP 84
Cdd:PRK07942   5 PGPLAAFDLETTGVDPETARIVTAALVVVDADGevVESREWLADPGVEIPEEASAVHGITTEYARAhgrpaAEVLAEIAD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  85 TLFERL-DGKLFVAHNASFDRGFLRAEFERAGIA-------FNPDVlctvrLSRALFP-REARHGLDALIERHGLVPAAR 155
Cdd:PRK07942  85 ALREAWaRGVPVVVFNAPYDLTVLDRELRRHGLPslvpgpvIDPYV-----IDKAVDRyRKGKRTLTALCEHYGVRLDNA 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499975509 156 HRALADA----DLLW---QFWRQLHEIVPLERLRDQI 185
Cdd:PRK07942 160 HEATADAlaaaRVAWalaRRFPELAALSPAELHELQA 196
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 15-162 1.38e-08

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 54.09  E-value: 1.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  15 LVFVDLETT-----GGSSAEHRITEIGVVEIGPLG--VSTWTTLVNPGQ--SIPPFIQQLTGISDDMVRDAPSFASLAPT 85
Cdd:COG5018    4 YLVIDLEATcwdgkPPPGFPMEIIEIGAVKVDENGeiIDEFSSFVKPVRrpKLSPFCTELTGITQEDVDSAPSFAEAIED 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  86 LFERL--DGKLFVAhNASFDRGFLRAEFERAGIAFnP------DVLctvRLSRALFPREARHGLDALIERHGLVPAAR-H 156
Cdd:COG5018   84 FKKWIgsEDYILCS-WGDYDRKQLERNCRFHGVPY-PfgdrhiNLK---KLFALYFGLKKRIGLKKALELLGLEFEGThH 158


                 ....*.
gi 499975509 157 RALADA 162
Cdd:COG5018  159 RALDDA 164
uvrC PRK00558
excinuclease ABC subunit UvrC;
203-285 2.19e-08

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 55.89  E-value: 2.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 203 LDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:PRK00558   8 LKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP 87


                 ...
gi 499975509 283 SHN 285
Cdd:PRK00558  88 RYN 90
uvrC TIGR00194
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ...
 203-302 6.11e-08

excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272953 [Multi-domain]  Cd Length: 574  Bit Score: 54.30  E-value: 6.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  203 LDTAPAGCGVYALFGEGDEALYVGRSVRVRQRLRALLTgERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:TIGR00194   5 LKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFR-ENNSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQP 83

                          90       100
                  ....*....|....*....|
gi 499975509  283 SHNRRPAADKaragnaGWPF 302
Cdd:TIGR00194  84 RYNVLLKDDK------GYPY 97
uvrC PRK14667
excinuclease ABC subunit C; Provisional
 200-287 9.15e-08

excinuclease ABC subunit C; Provisional


Pssm-ID: 237783 [Multi-domain]  Cd Length: 567  Bit Score: 53.97  E-value: 9.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 200 EAWLDTAPAGCGVYaLFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIAR 279
Cdd:PRK14667   7 LELIEKAPEEPGVY-LFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQ 85


                 ....*...
gi 499975509 280 LRPSHNRR 287
Cdd:PRK14667  86 YKPKYNVL 93
PRK09146 PRK09146
DNA polymerase III subunit epsilon; Validated
 6-203 3.32e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236392 [Multi-domain]  Cd Length: 239  Bit Score: 50.69  E-value: 3.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509   6 PSDPACEQPLVFVDLETTGGSSAEHRITEIGVV-----EIGPLGVSTWTtlVNPGQSIPPFIQQLTGISDDMVRDAPSFA 80
Cdd:PRK09146  40 PDTPLSEVPFVALDFETTGLDAEQDAIVSIGLVpftlqRIRCRQARHWV--VKPRRPLEEESVVIHGITHSELQDAPDLE 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  81 SLAPTLFERLDGKLFVAHNASFDRGFLRAEFER---AGIAFnPdVLCTVRLSRALFPREARHGLDALI------------ 145
Cdd:PRK09146 118 RILDELLEALAGKVVVVHYRRIERDFLDQALRNrigEGIEF-P-VIDTMEIEARIQRKQAGGLWNRLKgkkpesirlads 195

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499975509 146 -ERHGLVPAARHRALADAdllwqfwrqlheIVPLERLRDQIArttRHFRLAGGMTEAWL 203
Cdd:PRK09146 196 rLRYGLPAYSPHHALTDA------------IATAELLQAQIA---HHFSPDTPISKLWL 239
DNA_polA_I_Ecoli_like_exo cd06139
DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial ...
 80-185 3.89e-06

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: 47.13  E-value: 3.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  80 ASLAPtLFERlDGKLFVAHNASFDRGFLRAE-FERAGIAFnpDvlcTVRLSRALFPREARHGLDALIERH---------- 148
Cdd:cd06139   57 AALKP-LLED-PSIKKVGQNLKFDLHVLANHgIELRGPAF--D---TMLASYLLNPGRRRHGLDDLAERYlghktisfed 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499975509 149 --G-----------LVPAARHRALADADLLWQ----FWRQLHEIVPLERLRDQI 185
Cdd:cd06139  130 lvGkgkkqitfdqvPLEKAAEYAAEDADITLRlyelLKPKLKEEPGLLELYEEI 183
PRK05601 PRK05601
DNA polymerase III subunit epsilon; Validated
 14-114 2.23e-05

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235529 [Multi-domain]  Cd Length: 377  Bit Score: 45.98  E-value: 2.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  14 PLVFVDLETTGGSSAEHRITEIGVVEIGPLG--VSTWTTLVNPGQSIPPFiqQLTGISDDMVRDAPSFASLAPTLFERLD 91
Cdd:PRK05601  47 PFVAVSIQTSGIHPSTSRLITIDAVTLTADGeeVEHFHAVLNPGEDPGPF--HLHGLSAEEFAQGKRFSQILKPLDRLID 124

                         90       100
                 ....*....|....*....|...
gi 499975509  92 GKLFVAHNASFDRGFLRAEFERA 114
Cdd:PRK05601 125 GRTLILHNAPRTWGFIVSEAKRA 147
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 211-280 8.48e-05

GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.


Pssm-ID: 198380 [Multi-domain]  Cd Length: 69  Bit Score: 40.43  E-value: 8.48e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 211 GVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELgAMLAEAQWIARL 280
Cdd:cd00719    1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLKPFEILYLEVAPEAESE-LLDLEAALIKKL 69
PolA COG0749
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ...
 13-183 1.29e-04

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


Pssm-ID: 440512 [Multi-domain]  Cd Length: 575  Bit Score: 43.89  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  13 QPLVFVDLETTGGSSAEHRITEIGVVeigplgvstwttlVNPGQS--IPPFIQQLTGISDDMVRDApsfasLAPtLFERl 90
Cdd:COG0749    1 AGLVAFDTETTSLDPMDAELVGISFA-------------VEPGEAayIPLAHGAPEQLDLDEVLAA-----LKP-LLED- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  91 DGKLFVAHNASFDRGFLRaefeRAGIAFNPDVLCTVRLSRALFPREARHGLDALIERH-GLVP----------------- 152
Cdd:COG0749   61 PAIPKIGQNLKYDLHVLA----RYGIELAGVAFDTMLASYLLNPGRRRHGLDDLAERYlGHETisyeelagkgkkqltfd 136

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 499975509 153 ------AARHrALADADLLWQFWRQLHEIVPLERLRD 183
Cdd:COG0749  137 qvpleeAAEY-AAEDADITLRLHEVLKPELEEEGLLK 172
GIYc smart00465
GIY-YIG type nucleases (URI domain);
211-287 1.54e-04

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 40.10  E-value: 1.54e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499975509   211 GVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSK-EMRLAQQVRRVEWRETGNELGAML-AEAQWIARLRPSHNRR 287
Cdd:smart00465   3 GVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLlIDALLKYGGNFEFIILESFDESALeLEKYLIKEYKPKYNLL 81
RNaseT cd06134
DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' ...
 96-120 6.38e-04

DEDDh 3'-5' exonuclease domain of RNase T; RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.


Pssm-ID: 99837 [Multi-domain]  Cd Length: 189  Bit Score: 40.35  E-value: 6.38e-04
                         10        20
                 ....*....|....*....|....*
gi 499975509  96 VAHNASFDRGFLRAEFERAGIAFNP 120
Cdd:cd06134  106 VGHNAHFDLGFLNAAVARCKIKRNP 130
PRK05755 PRK05755
DNA polymerase I; Provisional
 39-174 1.61e-03

DNA polymerase I; Provisional


Pssm-ID: 235591 [Multi-domain]  Cd Length: 880  Bit Score: 40.46  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509  39 EIGPLGVSTWTTLVNPGQSippfiqQLTGIS-------------DDMVRDApsFASLAPtLFERlDGKLFVAHNASFDRG 105
Cdd:PRK05755 314 AAGLFAFDTETTSLDPMQA------ELVGLSfavepgeaayiplDQLDREV--LAALKP-LLED-PAIKKVGQNLKYDLH 383

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 106 FLRaefeRAGIAFNPDVLCTVRLSRALFPrEARHGLDALIERH---------------------GLVPAARHRALaDADL 164
Cdd:PRK05755 384 VLA----RYGIELRGIAFDTMLASYLLDP-GRRHGLDSLAERYlghktisfeevagkqltfaqvDLEEAAEYAAE-DADV 457

                        170
                 ....*....|
gi 499975509 165 LWQFWRQLHE 174
Cdd:PRK05755 458 TLRLHEVLKP 467
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 210-282 2.13e-03

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 36.55  E-value: 2.13e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499975509  210 CGVYALFGEGDEALYVGRSVRVRQRLRALLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRP 282
Cdd:pfam01541   2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHNAGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRP 74
uvrC PRK14669
excinuclease ABC subunit C; Provisional
 205-285 8.37e-03

excinuclease ABC subunit C; Provisional


Pssm-ID: 237784 [Multi-domain]  Cd Length: 624  Bit Score: 38.35  E-value: 8.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499975509 205 TAPAGCGVYALFGEGDEALYVGRSVRVRQRLRA-LLTGERRSSKEMRLAQQVRRVEWRETGNELGAMLAEAQWIARLRPS 283
Cdd:PRK14669   9 TLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSyFSEDKLGNIKTGSLIREAVDIDYILVDNEKEALALENNLIKQYKPR 88


                 ..
gi 499975509 284 HN 285
Cdd:PRK14669  89 FN 90
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH