ViewGene
Locus Name:
GeneID:
Location:

GeneID:3247
TrivialName: PA14_41050
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_41050
PAO1 Ortholog Locus:PA1816
Sequence Length:741
Protein Length:246
Start: 3661208
Stop: 3660468
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05205.1|AE004608_4 (AE004608) DNA polymerase III, epsilon chain [Pseudomonas aeruginosa PAO1]
Identities = 245/246 (99%), Positives = 246/246 (100%)
Sequence:
ATGCGTAGCGTCGTACTGGATACCGAAACCACCGGCATGCCGGTGACCGATGGTCACCGGATCATCGAGATC
GGCTGTGTCGAGCTGGAGGGGCGCCGCCTGACCGGTCGCCACTTCCACGTCTACCTGCAACCCGATCGCGAG
GTCGACGAAGGGGCGATCGCCGTCCACGGCATCACCAACGAATACCTGAAGGACAAGCCGCGCTTCCGCGAG
GTCGCCAACGATTTCTTCGAGTTCATCCGCGGCGCCCAACTGATCATCCATAACGCGGCGTTCGATATCGGC
TTCATCAACAACGAGTTCGCCCTGCTGGGCCAGCAGGACCGCTCGGACGTGAGCGAGTACTGCTCGGTGCTG
GATACCCTGCTGATGGCCCGCGAGCGCCATCCGGGTCAGCGCAACAACCTCGATGCGTTGTGCAAGCGCTAC
GGCGTGGACAACTCCGGCCGCGACCTGCACGGCGCGTTGCTCGACGCCGAGATCCTCGCCGACGTCTACCTG
GCGATGACCGGTGGCCAGACCAGCCTGTCGCTGGCCGGCAGCGGCGCGGAAGGCGACGGCAGCGGCCGGCCG
ATGGTCAGCCCGATCCGTCGGCTCGATCCGGCGCGGGTCGCCACCCCGGTGCTGCGCGCCAACGCCGAAGAG
CTGGCTGCGCATGCGGCGCGGCTGGCGGTGATCGAGAAGTCGGCAGGTGGTCCGTCGCTCTGGGCGCAACTG
GAAGCGCCGGTCGGCGAATAG
Translation:
MRSVVLDTETTGMPVTDGHRIIEIGCVELEGRRLTGRHFHVYLQPDREVDEGAIAVHGITNEYLKDKPRFRE
VANDFFEFIRGAQLIIHNAAFDIGFINNEFALLGQQDRSDVSEYCSVLDTLLMARERHPGQRNNLDALCKRY
GVDNSGRDLHGALLDAEILADVYLAMTGGQTSLSLAGSGAEGDGSGRPMVSPIRRLDPARVATPVLRANAEE
LAAHAARLAVIEKSAGGPSLWAQLEAPVGE*
AnnotationID:3255GeneID:3247
AnnotatorUID: diggins
Modification Date/Time: 2005-04-28 13:01:31
Gene Name:dnaQ
Confidence Code:2
GeneProduct:DNA polymerase III, epsilon chain
Cell Localization:()
Synonyms:mutD
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(18) Nucleotide biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0847,smart00479,pfam00929
Secondary Functional Category(ies):
EC Number:2.7.7.7
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO57180.1| (AE016869) DNA polymerase III, epsilon subunit [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 257

 Score =  364 bits (934), Expect = e-100
 Identities = 177/242 (73%), Positives = 205/242 (84%), Gaps = 3/242 (1%)

>gb|AAN69723.1|AE016608_9 (AE016789) DNA polymerase III, epsilon subunit [Pseudomonas putida
           KT2440]
          Length = 252

 Score =  353 bits (907), Expect = 4e-97
 Identities = 181/247 (73%), Positives = 208/247 (84%), Gaps = 5/247 (2%)

>gb|AAO10289.1|AE016803_76 (AE016803) DNA polymerase III, epsilon subunit [Vibrio vulnificus
           CMCP6]
          Length = 243

 Score =  259 bits (663), Expect = 7e-69
 Identities = 142/247 (57%), Positives = 173/247 (70%), Gaps = 23/247 (9%)






 
Structural Features:
COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases 
[DNA replication, recombination, and repair]
CD-Length = 243 residues,  94.7% aligned
Score =  188 bits (477), Expect = 7e-49
Identities = 87/241 (36%), Positives = 120/241 (49%), Gaps = 13/241 (5%)

smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and epsilon chain, 
ribonuclease T and other exonucleases
CD-Length = 171 residues,  96.5% aligned
Score =  148 bits (375), Expect = 6e-37
Identities = 61/171 (35%), Positives = 88/171 (51%), Gaps = 8/171 (4%)

pfam00929, Exonuc_X-T, Exonuclease.
CD-Length = 162 residues,  99.4% aligned
Score =  128 bits (323), Expect = 5e-31
Identities = 58/166 (34%), Positives = 91/166 (54%), Gaps = 7/166 (4%)






   
Genomic Context:






   
Comment:


















    ReferenceID:6497




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:23639




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36521




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3247_cdd.html


    		




 
URL:

















    ReferenceID:36591




  
Author/Investigator(s):
        Huang Y, Braithwaite DK, Ito J.





  
Title:
        Evolution of dnaQ, the gene encoding the editing 3' to 5' exonuclease subunit of DNA polymerase III holoenzyme in Gram-negative bacteria.




  
PubMed:
        9000520


MedLine:
        




    
Source:
FEBS Lett. 1997 Jan 2;400(1):94-8.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9000520

















    ReferenceID:36592




  
Author/Investigator(s):
        Cox EC, Horner DL.





  
Title:
        DNA sequence and coding properties of mutD(dnaQ) a dominant Escherichia coli mutator gene.




  
PubMed:
        3023634


MedLine:
        




    
Source:
J Mol Biol. 1986 Jul 5;190(1):113-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3023634









           
Homologs By Global Alignment 

           

       



     
Gene ID:3247
           
Identity:

                               
                                   0%
                               
                                   10%
                               
                                   20%
                               
                                   30%
                               
                                   40%
                               
                                   50%
                               
                                   60%
                               
                                   70%
                               
                                   80%
                               
                                   90%
                               
                                   100%
                               
                             

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
5223
                           PA1816_tr
                           translation of PA1816
                           246
                           99.59
                           99.99
                           0
                           1262.0
     

     
     
146234
                           gb|AAG05205.1|AE004608_4
                           (AE004608) DNA polymerase III, epsilon chain [Pseudomonas aeruginosa PAO1]
                           246
                           99.59
                           99.99
                           0
                           1262.0
     

     
     
146235
                           gb|AAF42851.1|
                           (AF220056) mismatch repair protein MutD [Pseudomonas aeruginosa]
                           246
                           99.59
                           99.99
                           0
                           1262.0
     

     
     
146236
                           gb|AAO57180.1|
                           (AE016869) DNA polymerase III, epsilon subunit [Pseudomonas syringae pv. tomato str. DC3000]
                           257
                           70.03
                           80.54
                           11
                           931.0
     

     
     
146237
                           gb|AAN69723.1|AE016608_9
                           (AE016789) DNA polymerase III, epsilon subunit [Pseudomonas putida KT2440]
                           257
                           70.03
                           81.32
                           16
                           916.0
     

     






      

          
GC ORFID: 46249How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1816Glimmer Score: 

          
Start: 1292702Stop: 1293442

          
Length: 741


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_PA1816 translation of PA1816Homolog Bit Score 490.0

          
Other Homologs:  t_PA1816 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCGTAGCGTCGTACTGGATACCGAAACCACCGGCATGCCGGTGACCGATGGTCACCGGATCATCGAGATC 
GGCTGTGTCGAGCTGGAGGGGCGCCGCCTGACCGGTCGCCACTTCCACGTCTACCTGCAACCCGATCGCGAG 
GTCGACGAAGGGGCGATCGCCGTCCACGGCATCACCAACGAATACCTGAAGGACAAGCCGCGCTTCCGCGAG 
GTCGCCAACGATTTCTTCGAGTTCATCCGCGGCGCCCAACTGATCATCCATAACGCGGCGTTCGATATCGGC 
TTCATCAACAACGAGTTCGCCCTGCTGGGCCAGCAGGACCGCTCGGACGTGAGCGAGTACTGCTCGGTGCTG 
GATACCCTGCTGATGGCCCGCGAGCGCCATCCGGGTCAGCGCAACAACCTCGATGCGTTGTGCAAGCGCTAC 
GGCGTGGACAACTCCGGCCGCGACCTGCACGGCGCGTTGCTCGACGCCGAGATCCTCGCCGACGTCTACCTG 
GCGATGACCGGTGGCCAGACCAGCCTGTCGCTGGCCGGCAGCGGCGCGGAAGGCGACGGCAGCGGCCGGCCG 
ATGGTCAGCCCGATCCGTCGGCTCGATCCGGCGCGGGTCGCCACCCCGGTGCTGCGCGCCAACGCCGAAGAG 
CTGGCTGCGCATGCGGCGCGGCTGGCGGTGATCGAGAAGTCGGCAGGTGGTCCGTCGCTCTGGGCGCAACTG 
GAAGCGCCGGTCGGCGAATAG