Conserved Protein Domain Family
DNA_polB_like1_exo

?
cd05782: DNA_polB_like1_exo 
Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases
A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Statistics
?
PSSM-Id: 99825
View PSSM: cd05782
Aligned: 32 rows
Threshold Bit Score: 173.58
Threshold Setting Gi: 163782354
Created: 15-Nov-2007
Updated: 2-Oct-2020
Structure
?
Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:The active site includes the catalytic site (characterized by four invariant acidic residues, DEDD) and the substrate (ssDNA) binding site.
  • Citation:PMID 9888810

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1           ####                                                                        
YP_742192     3 VLVFDIETVPDvvggrrllg---ldpslsdqEVAEAMMALrr-----------qsAGTDFQRLHL-----HRIVAISIAa 63  Alkalilimnicola ...
ZP_01251896  10 ILFLDIETVPEhsdfedlsp---tkqklftdKTEYQRKEDysp---------keyYERAGIWAEF-----GKIVCISVGy 72  Psychroflexus to...
ZP_02915295  10 ILFIDIETVPCvadye----------nltapQKLLWGKKAtllgatdtqeignlfSERAGVYAEF-----GKVIVIGLGh 74  Candidatus Amoeb...
ZP_01687853  16 ILFVDIKTVSQsdsyht--------lpqnlqKFWDKRFAYrrdedl---nieehyFQQASLQAEF-----GKIVTIGVGy 79  Microscilla mari...
YP_466044    25 FVTLDLETVPDealvsavdgepsrpyseqlrRVLAERRARt-------------gGRSDFLPLPY-----HRPVAACLLe 86  Anaeromyxobacter...
ZP_02177352   4 AIIFDIETVPTkeenlkeed---weyifkyaDTEEDREKQ---------------KERLSLWALT-----AHLVSVALLn 60  Hydrogenivirga s...
NP_662575     9 VVVFDVEWVPDpasgrriyk---ipdtasddEVLDVMWRKg-------------gATPDDPRPYLkt-vmCRVISIAALv 71  Chlorobium tepid...
YP_867537     9 VWAFDAEWTPDplagrmlyn---ldedltdaQVLAEMWKQg--------------GATEENPTPYlktalCRFISIAAVv 71  Magnetococcus sp...
ZP_01719392  11 ILFLDIETASLsdkfen--------lpprlqDEWIKKEKLiqtengk-iepgalyFDRAGIHAEF-----GQVICVGVGy 76  Algoriphagus sp....
ZP_01912745 129 TLVFDIETVPAvdleta--------pesvtkAVHRAADRYdg-----------dtSKVMGLSPFY-----GKVVSIAVGd 184 Plesiocystis pac...
Feature 1                                                                                       
YP_742192    64 d----ldRHGFRVws-------------lGDPEDDE--------------------AELIRRFFDGVERy----APRLVS 102 Alkalilimnicola ...
ZP_01251896  73 fn---fkGNERKFr---------------TTSFYGEe-------------------TDLLKRFKLLVENyfslpHHLMCG 115 Psychroflexus to...
ZP_02915295  75 itfdicgDPSLQVq---------------ALSSHNE--------------------KELLGQLRNILEEkyqqeNIRLCA 119 Candidatus Amoeb...
ZP_01687853  80 fyldehkETALRVk---------------AFAGADE--------------------KGLLEDFKALIDTkf-tdNLVMCA 123 Microscilla mari...
YP_466044    87 ae---edGGIVRV----------------TDAVAWTd------------------rRGPEAAFLETMWQrl--eGASLVT 127 Anaeromyxobacter...
ZP_02177352  61 ------vSEGLALvmylsdrdskeelelrEEFEGGElelrvhmvgfsmeegieeaeRRILTKFWKKAKEk---eGYRFVS 131 Hydrogenivirga s...
NP_662575    72 rkr-vkdGVTLKLi---------------SLPGLNVseq---------------aeGEIIRQFLEAVGKq----KAQIVG 116 Chlorobium tepid...
YP_867537    72 rr--qhqDGTITV----------------TLMSLPEevadtq--------apyakeDAVLSRFLQGVGEk----KPQLVG 121 Magnetococcus sp...
ZP_01719392  77 fqw-kkkDKKLIFr---------------SKVFSNEd------------------eRELLLDFNTLLEKk----KWILCA 118 Algoriphagus sp....
ZP_01912745 185 ge---dpDGPVTAlvva--------ppgrEDDAYPEwirp-------------mteAQLLRSFWHLADS-----AEVVVS 235 Plesiocystis pac...
Feature 1       ##  ###                                                           ##            
YP_742192   103 WNGGGFDLPVLHYRALLHGitaRRYWDSGqedrdfrfnnylNRFHDR-HTDLMDVLAGYqa-raNAPLDEIATLLGy-PG 179 Alkalilimnicola ...
ZP_01251896 116 HNAKEFDFPYIARRMLIRGialPSQLQFFg----------kKPWEIP-HLDTLELWKFGdy-khYTSLKLLTELFNipSP 183 Psychroflexus to...
ZP_02915295 120 HNGKEFDFPYLCRRMLVNGislPTVLDCAg----------kKPWEVT-HLDTMEMWRFGdr-ksFTSLDLLANLFGvnSS 187 Candidatus Amoeb...
ZP_01687853 124 HNGKEFDYPYLCRRMVIHGvelPLTLNLLh----------kKPWEIP-HLDTLEMWKFGdr-khKTSLSLLATLMDipEV 191 Microscilla mari...
YP_466044   128 FHGKGFDLPVLELRSLKHAiptPAWFGAA------------RRTGGTeHLDVKELLAGQa---tAAPLDLYAKLVGl-PG 191 Anaeromyxobacter...
ZP_02177352 132 FNGRGFDSVFLMLRSFVLGv-kVSRQFIG------------NRYEYRnHLDLLDLLSFHgq-grKYSLEFVCRRLGipSP 197 Hydrogenivirga s...
NP_662575   117 FNSSNADLPILYQRALANRvsaPTFCHRPdkpwe--gvdyfNRYSDF-SIDLKDLVGGYgk--aMPSLHELASSLGi-PG 190 Chlorobium tepid...
YP_867537   122 YNSISADIKAMLQRGIIRGmhqPKFAHRPnkpwe--gvdyfARGGDW-HVDLKEVVSGWgq--fTPSLHEMATLSGi-PG 195 Magnetococcus sp...
ZP_01719392 119 HNGKEFDFPYLCRRMLVQGvtlPEPLQIAg----------kKPWEVR-HLDTLELWKFGdy-khYTRLELLAAVFGipTS 186 Algoriphagus sp....
ZP_01912745 236 FNGRGFDVPFVQTRSLIHGv--PARVDLMs-----------SPFALRpHLDLYRLLAPNrgnpaSASLDVICWSLGieSP 302 Plesiocystis pac...
Feature 1                               #   #          
YP_742192   180 KMGMSGgKVWEAVQAGe-LGAVRDYCETDVLNTYLVWLR 217 Alkalilimnicola ehrlichei MLHE-1
ZP_01251896 184 KDDIDGsQVRDVFYKEkdLDRIVTYCEKDVIAVAQLILK 222 Psychroflexus torquis ATCC 700755
ZP_02915295 188 KTLMDGsEVSYFYYVEndLTRIAKYCMQDVIVTSQIFLK 226 Candidatus Amoebophilus asiaticus 5a2
ZP_01687853 192 ENRLEGqDINKVYHETqdMKQITQGCMRDIEILAKLFLK 230 Microscilla marina ATCC 23134
YP_466044   192 KEDVAGaDVQALYAEGa-LDRIAGYCMTDVVQTFLLFLR 229 Anaeromyxobacter dehalogenans 2CP-C
ZP_02177352 198 KEDMDGhDVKEYFAKGr-YRDIALYNLKDTIATARIYER 235 Hydrogenivirga sp. 128-5-R1-1
NP_662575   191 KMGIDGaDVIDLWRSGd-IRKIVEYNQFDALSTYLVWLR 228 Chlorobium tepidum TLS
YP_867537   196 KMDVAGdQVPQMWLDGr-LADIVAYNEFDALTTYLLWLR 233 Magnetococcus sp. MC-1
ZP_01719392 187 KDDLDGsQVNTTFHLEknINRIKKYCRKDVEVTARVYLA 225 Algoriphagus sp. PR1
ZP_01912745 303 KGEMDGsLVAPTYARGd-IEMIATYNVGDVRATRSVYRH 340 Plesiocystis pacifica SIR-1

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap