ViewGene
Locus Name:
GeneID:
Location:

GeneID:2039
TrivialName: PA14_20890
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_20890
PAO1 Ortholog Locus:PA3337
Sequence Length:999
Protein Length:332
Start: 1800156
Stop: 1801154
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06725.1|AE004756_3 (AE004756) ADP-L-glycero-D-mannoheptose 6-epimerase [Pseudomonas aeruginosa PAO1]
Identities = 331/332 (99%), Positives = 332/332 (100%)
Sequence:
GTGCCCATGAGCATCATCGTCACCGGCGCCGCCGGCTTCATCGGCAGCAATCTGCTGCAGGCGCTGAACCGG
CGCGGCGAGACCGACATCATCGCGGTGGACGATCTCACCGACGGCGAGCAGTTCCGCAACCTGGCGGACGCC
GATATCGCCGACTACCTGGACCAGAACGACTTCCTCGAGCGTTACGCCCGCGGCGACTTCGGCACGGTCCGC
GCGCTGTTCCACCAGGGTGCCTGCGCCAGCACCCTGGAAAGCAATGGCCGCTACATGATGGAGAACAACTAC
CGCTACAGTTGCCGCCTGCTGGAAAGCAGCCTGGAACTCGGCGTGCCGTTCCTCTACGCCTCGTCGGCGGCG
GTCTACGGAGCCGGCCGGACCTTCCGCGAGGCGCGCCAGTACGAGCGGCCGCTGAACGTCTACGGCTATTCC
AAGTTCCTCTTCGACCAGCGTGTGCGGCGGGCGCTGCCGCAGGCGCGCAGCCAGGTGGTCGGCCTGCGTTAC
TTCAACGTCTACGGGCCGCGCGAGGAACACAAGGGGCGGATGGCCTCGGTGGCCTACCACTGCTACCAGCAA
TTGCGCCGCGACGGGCGGGTCGAACTGTTCGGCGAACACGGTGGCTTCCCGCCCGGCGGCCACCTGCGCGAC
TTTGTCGCGGTGGAGGACGTGGCGCGGGTCAACCTGCATTTCTTCGATCATCCGCAGCGTTCGGGAATCTTC
AACCTCGGCAGCGGCCAGGCGCGGACCTTCAACGAGGTCGCCCTGGCGGTGATCAATAGCGTCCGCGCCAAT
GCCGACCAGCCGCCCCTGTCGCTGCAGCAGGCGGTGGAAAGCGGCCTGCTCGGCTACCGCGAGTTCCCCGAG
TCGCTGCGGGCGCGCTACCAGAGCCACACCTGCGCCGACCTGGAGCTGCTGCGCGAGGCGGGCTACCGCGAC
GATTTCCAGAGCCTGGAAGAGGGCGTCGCCGGCTACTGCCGCTGGCTGGCGCGCAGCGCCTGA
Translation:
MPMSIIVTGAAGFIGSNLLQALNRRGETDIIAVDDLTDGEQFRNLADADIADYLDQNDFLERYARGDFGTVR
ALFHQGACASTLESNGRYMMENNYRYSCRLLESSLELGVPFLYASSAAVYGAGRTFREARQYERPLNVYGYS
KFLFDQRVRRALPQARSQVVGLRYFNVYGPREEHKGRMASVAYHCYQQLRRDGRVELFGEHGGFPPGGHLRD
FVAVEDVARVNLHFFDHPQRSGIFNLGSGQARTFNEVALAVINSVRANADQPPLSLQQAVESGLLGYREFPE
SLRARYQSHTCADLELLREAGYRDDFQSLEEGVAGYCRWLARSA*
AnnotationID:2047GeneID:2039
AnnotatorUID: diggins
Modification Date/Time: 2005-04-15 09:09:32
Gene Name:rfaD
Confidence Code:2
GeneProduct:ADP-L-glycero-D-mannoheptose 6-epimerase
Cell Localization:()
Synonyms:gmhD
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:ADP-glycero-mannoheptose epimerase
Functional Category Confidence Code:5
COGs:COG0451,pfam01370,COG1087
Secondary Functional Category(ies):carbon compound metabolism
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>emb|CAD14617.1| (AL646061) PROBABLE ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
           PROTEIN [Ralstonia solanacearum]
          Length = 331

 Score =  439 bits (1130), Expect = e-123
 Identities = 206/326 (63%), Positives = 265/326 (81%)

>gb|AAF41240.1| (AE002436) ADP-L-glycero-D-mannoheptose-6-epimerase [Neisseria
           meningitidis MC58]
          Length = 334

 Score =  372 bits (956), Expect = e-102
 Identities = 180/329 (54%), Positives = 249/329 (75%), Gaps = 3/329 (0%)

>gb|AAA79173.1| (L07845) ADP-L-glycero-D-mannoheptose epimerase [Neisseria
           gonorrhoeae]
          Length = 334

 Score =  370 bits (951), Expect = e-102
 Identities = 180/329 (54%), Positives = 247/329 (75%), Gaps = 3/329 (0%)






 
Structural Features:
COG0451, WcaG, Nucleoside-diphosphate-sugar epimerases 
[Cell envelope biogenesis, outer membrane / 
Carbohydrate transport and metabolism] 
CD-Length = 314 residues,  98.1% aligned
Score =  151 bits (381), Expect = 1e-37
Identities = 102/334 (30%), Positives = 143/334 (42%), Gaps = 34/334 (10%)

pfam01370, Epimerase, NAD dependent epimerase/dehydratase family. 
CD-Length = 310 residues,  98.4% aligned
Score =  112 bits (282), Expect = 5e-26
Identities = 85/340 (25%), Positives = 136/340 (40%), Gaps = 52/340 (15%)

COG1087, GalE, UDP-glucose 4-epimerase 
CD-Length = 329 residues,  81.2% aligned
Score = 99.1 bits (247), Expect = 6e-22
Identities = 76/275 (27%), Positives = 129/275 (46%), Gaps = 28/275 (10%)






   
Genomic Context:






   
Comment:


















    ReferenceID:14487




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21227




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32228




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2039_cdd.html


    		




 
URL:

















    ReferenceID:33998




  
Author/Investigator(s):
        Sirisena DM, MacLachlan PR, Liu SL, Hessel A, Sanderson KE.





  
Title:
        Molecular analysis of the rfaD gene, for heptose synthesis, and the rfaF gene, for heptose transfer, in lipopolysaccharide synthesis in Salmonella typhimurium.




  
PubMed:
        8157607


MedLine:
        




    
Source:
J Bacteriol. 1994 Apr;176(8):2379-85.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8157607

















    ReferenceID:33999




  
Author/Investigator(s):
        Raina S, Georgopoulos C.





  
Title:
        The htrM gene, whose product is essential for Escherichia coli viability only at elevated temperatures, is identical to the rfaD gene.




  
PubMed:
        1861974


MedLine:
        




    
Source:
Nucleic Acids Res. 1991 Jul 25;19(14):3811-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1861974

















    ReferenceID:34000




  
Author/Investigator(s):
        Pegues JC, Chen LS, Gordon AW, Ding L, Coleman WG Jr.





  
Title:
        Cloning, expression, and characterization of the Escherichia coli K-12 rfaD gene.




  
PubMed:
        2198271


MedLine:
        




    
Source:
J Bacteriol. 1990 Aug;172(8):4652-60.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2198271

















    ReferenceID:34001




  
Author/Investigator(s):
        Coleman WG Jr.





  
Title:
        The rfaD gene codes for ADP-L-glycero-D-mannoheptose-6-epimerase. An enzyme required for lipopolysaccharide core biosynthesis.




  
PubMed:
        6337148


MedLine:
        




    
Source:
J Biol Chem. 1983 Feb 10;258(3):1985-90.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6337148









           
Homologs By Global Alignment 

           

       



     
Gene ID:2039
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3533
                           PA3337_tr
                           translation of PA3337
                           332
                           99.69
                           99.99
                           0
                           1728.0
     

     
     
109043
                           gb|AAG06725.1|AE004756_3
                           (AE004756) ADP-L-glycero-D-mannoheptose 6-epimerase [Pseudomonas aeruginosa PAO1]
                           332
                           99.39
                           99.99
                           0
                           1725.0
     

     
     
109044
                           emb|CAD14617.1|
                           (AL646061) PROBABLE ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE PROTEIN [Ralstonia solanacearum]
                           333
                           62.46
                           80.48
                           3
                           1128.0
     

     
     
109045
                           gb|AAD43346.1|AF159428_3
                           (AF159428) putative ADP-glycero-mannoheptose epimerase [Burkholderia pseudomallei]
                           332
                           59.93
                           78.01
                           2
                           1084.0
     

     
     
109051
                           emb|CAE38408.1|
                           (BX640432) ADP-L-glycero-D-manno-heptose-6-epimerase [Bordetella parapertussis]
                           333
                           54.65
                           68.76
                           5
                           925.0
     

     






      

          
GC ORFID: 45041How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3337Glimmer Score: 

          
Start: 3153776Stop: 3152778

          
Length: 999


          
Start Codon: GTGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3337 translation of PA3337Homolog Bit Score 670.0

          
Other Homologs:  t_PA3337 (ORF: GLIMMER)

          
GC ORF Sequence

           
GTGCCCATGAGCATCATCGTCACCGGCGCCGCCGGCTTCATCGGCAGCAATCTGCTGCAGGCGCTGAACCGG 
CGCGGCGAGACCGACATCATCGCGGTGGACGATCTCACCGACGGCGAGCAGTTCCGCAACCTGGCGGACGCC 
GATATCGCCGACTACCTGGACCAGAACGACTTCCTCGAGCGTTACGCCCGCGGCGACTTCGGCACGGTCCGC 
GCGCTGTTCCACCAGGGTGCCTGCGCCAGCACCCTGGAAAGCAATGGCCGCTACATGATGGAGAACAACTAC 
CGCTACAGTTGCCGCCTGCTGGAAAGCAGCCTGGAACTCGGCGTGCCGTTCCTCTACGCCTCGTCGGCGGCG 
GTCTACGGAGCCGGCCGGACCTTCCGCGAGGCGCGCCAGTACGAGCGGCCGCTGAACGTCTACGGCTATTCC 
AAGTTCCTCTTCGACCAGCGTGTGCGGCGGGCGCTGCCGCAGGCGCGCAGCCAGGTGGTCGGCCTGCGTTAC 
TTCAACGTCTACGGGCCGCGCGAGGAACACAAGGGGCGGATGGCCTCGGTGGCCTACCACTGCTACCAGCAA 
TTGCGCCGCGACGGGCGGGTCGAACTGTTCGGCGAACACGGTGGCTTCCCGCCCGGCGGCCACCTGCGCGAC 
TTTGTCGCGGTGGAGGACGTGGCGCGGGTCAACCTGCATTTCTTCGATCATCCGCAGCGTTCGGGAATCTTC 
AACCTCGGCAGCGGCCAGGCGCGGACCTTCAACGAGGTCGCCCTGGCGGTGATCAATAGCGTCCGCGCCAAT 
GCCGACCAGCCGCCCCTGTCGCTGCAGCAGGCGGTGGAAAGCGGCCTGCTCGGCTACCGCGAGTTCCCCGAG 
TCGCTGCGGGCGCGCTACCAGAGCCACACCTGCGCCGACCTGGAGCTGCTGCGCGAGGCGGGCTACCGCGAC 
GATTTCCAGAGCCTGGAAGAGGGCGTCGCCGGCTACTGCCGCTGGCTGGCGCGCAGCGCCTGA