ViewGene
Locus Name:
GeneID:
Location:

GeneID:1032
TrivialName: PA14_66060
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_66060
PAO1 Ortholog Locus:PA4996
Sequence Length:1425
Protein Length:474
Start: 5885089
Stop: 5883665
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08381.1|AE004912_7 (AE004912) LPS biosynthesis protein RfaE [Pseudomonas aeruginosa PAO1]
Identities = 473/474 (99%), Positives = 473/474 (99%)
Sequence:
ATGAAGTTGTCCATGCCCCGTTTCGACCAGGCCCCGGTGTTGGTGGTCGGTGATGTGATGCTTGACCGCTAC
TGGCATGGCGCGACTTCGCGCATTTCGCCGGAGGCCCCGGTGCCGGTGGTCCGCGTCGAACAGCACGAGGAC
CGCCCCGGCGGCGCCGCCAACGTCGCGCTGAACATCGCCGCGCTGGGCGCACAGGCCTTGCTGGTCGGCGTC
ACCGGCCGCGACGAGGCCGCCGACAGCCTGGCCAACAGCCTCAAGGCCGCTGGAGTGGACGCGCGCTTCCAG
CGCATCGATAGCCAGCCGACCATCGTCAAGCTGCGGGTCATGAGTCGTCACCAGCAACTGCTGCGGGTCGAC
TTCGAGGAACCGTTCCGCACCGACGCGGCGGCCCTGGCCGTGGACGTCGAGTCGCTGCTGGCCAAGGTCAAG
GTGCTGGTGCTGTCCGACTACGGCAAGGGCGCGCTACAGAACCACCAGGTGCTGATCCAGGCGGCGCGGGCG
CGCAACATTCCGGTACTGGCCGATCCCAAGGGCAAGGACTTCGCCATCTATCGCGGCGCCAGCCTGATCACC
CCGAACCTGTCCGAATTCGAGACCATCGTCGGCCGTTGCGCCGACGAAGCCGAACTGGTCGCCAAGGGCCAG
GAGCTGATGAGCGAACTCGACCTCGGCGCCTTGCTGGTGACCCGCGGCGAGCATGGCATGACCCTGCTCCGC
CATGGCCAGCCGGCCCTGCACCTGCCGGCGCGGGCGCGGGAAGTGTTCGACGTCACCGGTGCTGGCGATACG
GTCATCTCCACCCTGGCCGCGGCGCTTGCCGCCGGCGAGGAGCTGCCGTCCGCGGTGGGCCTGGCCAACCTG
GCCGCCGGCATCGTGGTCGGCAAGCTGGGTACCGCGGCGATCAGCGCGCCCGAACTGCGTCGCGCGGTGCAG
CGCGAGCAGGGTTCCGAGCGTGGCGTGCTGGGCCTGGAGCAACTGCTGCTGGCAATCGAAGACGCCCGCGCC
CACGGCGAGAAGATCGTCTTCACCAATGGCTGCTTCGACATCCTTCACGCCGGCCACGTGACCTACCTCGAA
CAGGCGCGCGCCCAGGGCGACCGCCTGATCGTCGGGGTCAACGACGACGCCTCGGTCACTCGCCTGAAGGGC
GTTGGCCGGCCGATCAACTCGGTGGACCGGCGCATGGCGGTACTCGCCGGGCTCGGCGCGGTGGACTGGGTG
GTGAGCTTCGCCGAAGACACTCCCGAGCGCCTGCTCGAGCAGGTGCGTCCGGACGTGCTGGTCAAGGGCGGC
GATTACGGCGTCGAGCAGGTGGTCGGCGCGCAGATCGTCAAGGCTTACGGCGGCGAGGTACGGGTGCTCGGC
CTGGTGGAGAACAGCTCCACCACCGCCATCGTCGAGAAGATCCGCCAGAAAGGCTGA
Translation:
MKLSMPRFDQAPVLVVGDVMLDRYWHGATSRISPEAPVPVVRVEQHEDRPGGAANVALNIAALGAQALLVGV
TGRDEAADSLANSLKAAGVDARFQRIDSQPTIVKLRVMSRHQQLLRVDFEEPFRTDAAALAVDVESLLAKVK
VLVLSDYGKGALQNHQVLIQAARARNIPVLADPKGKDFAIYRGASLITPNLSEFETIVGRCADEAELVAKGQ
ELMSELDLGALLVTRGEHGMTLLRHGQPALHLPARAREVFDVTGAGDTVISTLAAALAAGEELPSAVGLANL
AAGIVVGKLGTAAISAPELRRAVQREQGSERGVLGLEQLLLAIEDARAHGEKIVFTNGCFDILHAGHVTYLE
QARAQGDRLIVGVNDDASVTRLKGVGRPINSVDRRMAVLAGLGAVDWVVSFAEDTPERLLEQVRPDVLVKGG
DYGVEQVVGAQIVKAYGGEVRVLGLVENSSTTAIVEKIRQKG*
AnnotationID:1041GeneID:1032
AnnotatorUID: diggins
Modification Date/Time: 2005-03-14 09:09:46
Gene Name:rfaE
Confidence Code:2
GeneProduct:lipopolysaccharide biosynthesis protein RfaE
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(7) Cell wall / LPS / capsule
Alternate Gene Product Name:ADP-heptose synthase
Functional Category Confidence Code:5
COGs:COG2870
Secondary Functional Category(ies):cell envelope biogenesis, outer membrane
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70501.1|AE016691_9 (AE016792) lipopolysaccharide core biosynthesis protein
           [Pseudomonas putida KT2440]
          Length = 473

 Score =  798 bits (2061), Expect = 0.0

>gb|AAO58411.1| (AE016874) lipopolysaccharide biosynthesis protein RfaE
           [Pseudomonas syringae pv. tomato str. DC3000]
          Length = 474

 Score =  794 bits (2051), Expect = 0.0
 Identities = 412/474 (86%), Positives = 434/474 (91%)

>gb|AAN56728.1|AE015808_4 (AE015808) ADP-heptose synthase [Shewanella oneidensis MR-1]
          Length = 476

 Score =  540 bits (1390), Expect = e-152
 Identities = 280/475 (58%), Positives = 352/475 (74%), Gaps = 2/475 (0%)








 
Structural Features:
COG2870, RfaE, ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase 
[Cell envelope biogenesis, outer membrane]
CD-Length = 467 residues, 100.0% aligned
Score =  661 bits (1707), Expect = 0.0
Identities = 302/475 (63%), Positives = 348/475 (73%), Gaps = 9/475 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:2067




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:19209




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35070




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1032_cdd.html


    		




 
URL:

















    ReferenceID:35875




  
Author/Investigator(s):
        Jin UH, Chung TW, Lee YC, Ha SD, Kim CH.





  
Title:
        Molecular cloning and functional expression of the rfaE gene required for lipopolysaccharide biosynthesis in Salmonella typhimurium.




  
PubMed:
        12441667


MedLine:
        




    
Source:
Glycoconj J. 2001 Oct;18(10):779-87.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12441667

















    ReferenceID:35876




  
Author/Investigator(s):
        Valvano MA, Marolda CL, Bittner M, Glaskin-Clay M, Simon TL, Klena JD.





  
Title:
        The rfaE gene from Escherichia coli encodes a bifunctional protein involved in biosynthesis of the lipopolysaccharide core precursor ADP-L-glycero-D-manno-heptose.




  
PubMed:
        10629197


MedLine:
        




    
Source:
J Bacteriol. 2000 Jan;182(2):488-97.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10629197

















    ReferenceID:35877




  
Author/Investigator(s):
        Lee NG, Sunshine MG, Apicella MA.





  
Title:
        Molecular cloning and characterization of the nontypeable Haemophilus influenzae 2019 rfaE gene required for lipopolysaccharide biosynthesis.




  
PubMed:
        7868252


MedLine:
        




    
Source:
nfect Immun. 1995 Mar;63(3):818-24.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7868252









           
Homologs By Global Alignment 

           

       



     
Gene ID:1032
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
1854
                           PA4996_tr
                           translation of PA4996
                           474
                           99.78
                           99.78
                           0
                           2342.0
     

     
     
64244
                           gb|AAG08381.1|AE004912_7
                           (AE004912) LPS biosynthesis protein RfaE [Pseudomonas aeruginosa PAO1]
                           474
                           99.78
                           99.78
                           0
                           2342.0
     

     
     
64246
                           gb|AAO58411.1|
                           (AE016874) lipopolysaccharide biosynthesis protein RfaE [Pseudomonas syringae pv. tomato str. DC3000]
                           474
                           86.91
                           91.56
                           0
                           2051.0
     

     
     
64245
                           gb|AAN70501.1|AE016691_9
                           (AE016792) lipopolysaccharide core biosynthesis protein [Pseudomonas putida KT2440]
                           474
                           86.70
                           92.61
                           1
                           2061.0
     

     
     
64247
                           gb|AAN56728.1|AE015808_4
                           (AE015808) ADP-heptose synthase [Shewanella oneidensis MR-1]
                           476
                           58.82
                           73.94
                           2
                           1392.0
     

     






      

          
GC ORFID: 44034How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4996Glimmer Score: 

          
Start: 5148772Stop: 5147348

          
Length: 1425


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4996 translation of PA4996Homolog Bit Score 906.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3401 (ORF: BLASTX 791.0), t_PA4996 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAAGTTGTCCATGCCCCGTTTCGACCAGGCCCCGGTGTTGGTGGTCGGTGATGTGATGCTTGACCGCTAC 
TGGCATGGCGCGACTTCGCGCATTTCGCCGGAGGCCCCGGTGCCGGTGGTCCGCGTCGAACAGCACGAGGAC 
CGCCCCGGCGGCGCCGCCAACGTCGCGCTGAACATCGCCGCGCTGGGCGCACAGGCCTTGCTGGTCGGCGTC 
ACCGGCCGCGACGAGGCCGCCGACAGCCTGGCCAACAGCCTCAAGGCCGCTGGAGTGGACGCGCGCTTCCAG 
CGCATCGATAGCCAGCCGACCATCGTCAAGCTGCGGGTCATGAGTCGTCACCAGCAACTGCTGCGGGTCGAC 
TTCGAGGAACCGTTCCGCACCGACGCGGCGGCCCTGGCCGTGGACGTCGAGTCGCTGCTGGCCAAGGTCAAG 
GTGCTGGTGCTGTCCGACTACGGCAAGGGCGCGCTACAGAACCACCAGGTGCTGATCCAGGCGGCGCGGGCG 
CGCAACATTCCGGTACTGGCCGATCCCAAGGGCAAGGACTTCGCCATCTATCGCGGCGCCAGCCTGATCACC 
CCGAACCTGTCCGAATTCGAGACCATCGTCGGCCGTTGCGCCGACGAAGCCGAACTGGTCGCCAAGGGCCAG 
GAGCTGATGAGCGAACTCGACCTCGGCGCCTTGCTGGTGACCCGCGGCGAGCATGGCATGACCCTGCTCCGC 
CATGGCCAGCCGGCCCTGCACCTGCCGGCGCGGGCGCGGGAAGTGTTCGACGTCACCGGTGCTGGCGATACG 
GTCATCTCCACCCTGGCCGCGGCGCTTGCCGCCGGCGAGGAGCTGCCGTCCGCGGTGGGCCTGGCCAACCTG 
GCCGCCGGCATCGTGGTCGGCAAGCTGGGTACCGCGGCGATCAGCGCGCCCGAACTGCGTCGCGCGGTGCAG 
CGCGAGCAGGGTTCCGAGCGTGGCGTGCTGGGCCTGGAGCAACTGCTGCTGGCAATCGAAGACGCCCGCGCC 
CACGGCGAGAAGATCGTCTTCACCAATGGCTGCTTCGACATCCTTCACGCCGGCCACGTGACCTACCTCGAA 
CAGGCGCGCGCCCAGGGCGACCGCCTGATCGTCGGGGTCAACGACGACGCCTCGGTCACTCGCCTGAAGGGC 
GTTGGCCGGCCGATCAACTCGGTGGACCGGCGCATGGCGGTACTCGCCGGGCTCGGCGCGGTGGACTGGGTG 
GTGAGCTTCGCCGAAGACACTCCCGAGCGCCTGCTCGAGCAGGTGCGTCCGGACGTGCTGGTCAAGGGCGGC 
GATTACGGCGTCGAGCAGGTGGTCGGCGCGCAGATCGTCAAGGCTTACGGCGGCGAGGTACGGGTGCTCGGC 
CTGGTGGAGAACAGCTCCACCACCGCCATCGTCGAGAAGATCCGCCAGAAAGGCTGA