ViewGene
Locus Name:
GeneID:
Location:

GeneID:2744
TrivialName: PA14_69690
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_69690
PAO1 Ortholog Locus:PA5278
Sequence Length:831
Protein Length:276
Start: 6215945
Stop: 6216775
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08663.1|AE004940_7 (AE004940) diaminopimelate epimerase [Pseudomonas aeruginosa PAO1]
Identities = 275/276 (99%), Positives = 276/276 (100%)
Sequence:
ATGCTTTTGCGCTTCACCAAGATGCATGGCCTGGGCAACGACTTCATGGTCCTCGACCTGGTCAGCCAGCAC
GCCCATGTGCAGCCCAAGCACGTCAAGCTCTGGGGCGACCGCAACACCGGGGTCGGCTTCGACCAGTTGCTG
ATCGTCGAAGCCCCGAGCAGCCCCGACGTCGACTTCCGCTACCGGATTTTCAACGCCGACGGCTCCGAGGTC
GAGCAGTGCGGCAACGGCGCCCGCTGCTTCGCCCGCTTCGTTCAGGACAAGCGCCTGACGGTGAAGAAGAGC
ATCCGCGTAGAAACCAAGGGCGGCATCATCGAGCTGAATATCCGCCCGGACGGCCAGGTCACGGTGGACATG
GGTCCGCCGCGCCTGGCCCCGGCCGAGATACCGTTCCAGGCCGAGCGCGAAGCCTTGTCCTATGAGATAGAG
GTGAATGGCCAGCGCGTCGAACTGGCCGCGGTATCCATGGGCAATCCCCATGGCGTGCTGCGCGTCGAGAAC
GTCGACAGCGCACCGGTACACAGCCTCGGTCCGCAACTGGAAGTCCATCCGCGCTTCCCGAAGAAGGCCAAC
ATCGGCTTCCTCCAGGTGCTCGATCCGCACCATGCGCGCCTGCGCGTCTGGGAGCGCGGCGTCGGCGAGACC
CAGGCCTGCGGCACCGGCGCCTGCGCCGCGGCGGTTGCCGGGATTCGCCAGGGCTGGCTGCAATCGCCGGTG
CAGATCGACCTCCCCGGCGGCCGCCTGCACATCGAGTGGGCAGGTCCCGGCCAGCCCGTTATGATGACCGGG
CCTGCCGTCCGCGTGTATGAAGGCCAGGTCCGCCTGTAA
Translation:
MLLRFTKMHGLGNDFMVLDLVSQHAHVQPKHVKLWGDRNTGVGFDQLLIVEAPSSPDVDFRYRIFNADGSEV
EQCGNGARCFARFVQDKRLTVKKSIRVETKGGIIELNIRPDGQVTVDMGPPRLAPAEIPFQAEREALSYEIE
VNGQRVELAAVSMGNPHGVLRVENVDSAPVHSLGPQLEVHPRFPKKANIGFLQVLDPHHARLRVWERGVGET
QACGTGACAAAVAGIRQGWLQSPVQIDLPGGRLHIEWAGPGQPVMMTGPAVRVYEGQVRL*
AnnotationID:2752GeneID:2744
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 14:02:32
Gene Name:dapF
Confidence Code:2
GeneProduct:diaminopimelate epimerase
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(2) Amino acid biosynthesis and metabolism
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG0253
Secondary Functional Category(ies):
EC Number:5.1.1.7
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70793.1|AE016723_5 (AE016793) diaminopimelate epimerase [Pseudomonas putida KT2440]
          Length = 287

 Score =  466 bits (1199), Expect = e-131
 Identities = 219/276 (79%), Positives = 246/276 (89%)

>gb|AAO53770.1| (AE016856) diaminopimelate epimerase [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 276

 Score =  466 bits (1198), Expect = e-131
 Identities = 218/276 (78%), Positives = 245/276 (88%)

>gb|AAL22791.1| (AE008884) diaminopimelate epimerase [Salmonella typhimurium LT2]
          Length = 275

 Score =  325 bits (834), Expect = 1e-88
 Identities = 154/275 (56%), Positives = 201/275 (73%)









 
Structural Features:
COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]
CD-Length = 272 residues, 100.0% aligned
Score =  361 bits (929), Expect = 4e-101
Identities = 141/274 (51%), Positives = 178/274 (64%), Gaps = 2/274 (0%)






   
Genomic Context:






   
Comment:


















    ReferenceID:5491




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:22635




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34806




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2744_cdd.html


    		




 
URL:

















    ReferenceID:35720




  
Author/Investigator(s):
        Hofte M, Dong Q, Kourambas S, Krishnapillai V, Sherratt D, Mergeay M.





  
Title:
        The sss gene product, which affects pyoverdin production in Pseudomonas aeruginosa 7NSK2, is a site-specific recombinase.




  
PubMed:
        7715441


MedLine:
        




    
Source:
Mol Microbiol. 1994 Dec;14(5):1011-20.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7715441

















    ReferenceID:35721




  
Author/Investigator(s):
        Hartmann M, Tauch A, Eggeling L, Bathe B, Mockel B, Puhler A, Kalinowski J.





  
Title:
        Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum.




  
PubMed:
        12948639


MedLine:
        




    
Source:
J Biotechnol. 2003 Sep 4;104(1-3):199-211.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12948639

















    ReferenceID:35722




  
Author/Investigator(s):
        Richaud C, Printz C.





  
Title:
        Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12.




  
PubMed:
        3057443


MedLine:
        




    
Source:
Nucleic Acids Res. 1988 Nov 11;16(21):10367.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=3057443









           
Homologs By Global Alignment 

           

       



     
Gene ID:2744
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
4477
                           PA5278_tr
                           translation of PA5278
                           276
                           99.63
                           99.99
                           0
                           1457.0
     

     
     
129566
                           gb|AAG08663.1|AE004940_7
                           (AE004940) diaminopimelate epimerase [Pseudomonas aeruginosa PAO1]
                           276
                           99.63
                           99.99
                           0
                           1457.0
     

     
     
129567
                           emb|CAA72944.1|
                           (Y12268) DapF protein [Pseudomonas fluorescens]
                           276
                           79.71
                           89.49
                           0
                           1204.0
     

     
     
129569
                           gb|AAO53770.1|
                           (AE016856) diaminopimelate epimerase [Pseudomonas syringae pv. tomato str. DC3000]
                           276
                           78.98
                           88.76
                           0
                           1198.0
     

     
     
129568
                           gb|AAN70793.1|AE016723_5
                           (AE016793) diaminopimelate epimerase [Pseudomonas putida KT2440]
                           287
                           76.30
                           85.71
                           11
                           1199.0
     

     






      

          
GC ORFID: 45746How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5278Glimmer Score: 

          
Start: 5479632Stop: 5480462

          
Length: 831


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA5278 translation of PA5278Homolog Bit Score 565.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3115 (ORF: BLASTX 456.0), t_PA5278 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGCTTTTGCGCTTCACCAAGATGCATGGCCTGGGCAACGACTTCATGGTCCTCGACCTGGTCAGCCAGCAC 
GCCCATGTGCAGCCCAAGCACGTCAAGCTCTGGGGCGACCGCAACACCGGGGTCGGCTTCGACCAGTTGCTG 
ATCGTCGAAGCCCCGAGCAGCCCCGACGTCGACTTCCGCTACCGGATTTTCAACGCCGACGGCTCCGAGGTC 
GAGCAGTGCGGCAACGGCGCCCGCTGCTTCGCCCGCTTCGTTCAGGACAAGCGCCTGACGGTGAAGAAGAGC 
ATCCGCGTAGAAACCAAGGGCGGCATCATCGAGCTGAATATCCGCCCGGACGGCCAGGTCACGGTGGACATG 
GGTCCGCCGCGCCTGGCCCCGGCCGAGATACCGTTCCAGGCCGAGCGCGAAGCCTTGTCCTATGAGATAGAG 
GTGAATGGCCAGCGCGTCGAACTGGCCGCGGTATCCATGGGCAATCCCCATGGCGTGCTGCGCGTCGAGAAC 
GTCGACAGCGCACCGGTACACAGCCTCGGTCCGCAACTGGAAGTCCATCCGCGCTTCCCGAAGAAGGCCAAC 
ATCGGCTTCCTCCAGGTGCTCGATCCGCACCATGCGCGCCTGCGCGTCTGGGAGCGCGGCGTCGGCGAGACC 
CAGGCCTGCGGCACCGGCGCCTGCGCCGCGGCGGTTGCCGGGATTCGCCAGGGCTGGCTGCAATCGCCGGTG 
CAGATCGACCTCCCCGGCGGCCGCCTGCACATCGAGTGGGCAGGTCCCGGCCAGCCCGTTATGATGACCGGG 
CCTGCCGTCCGCGTGTATGAAGGCCAGGTCCGCCTGTAA