ViewGene
Locus Name:
GeneID:
Location:

GeneID:829
TrivialName: PA14_57940
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_57940
PAO1 Ortholog Locus:PA4462
Sequence Length:1494
Protein Length:497
Start: 5156461
Stop: 5157954
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07850.1|AE004860_6 (AE004860) RNA polymerase sigma-54 factor [Pseudomonas aeruginosa PAO1]
Identities = 497/497 (100%), Positives = 497/497 (100%)
Sequence:
ATGAAACCATCGCTAGTCCTCAAGATGGGCCAGCAGCTGACGATGACGCCGCAGCTGCAACAGGCCATACGC
CTCCTCCAGCTATCCACCCTGGACCTCCAGCAGGAAATCCAGGAAGCGCTGGAATCCAATCCCATGCTCGAA
CGCCAGGAAGACGGCGACGATTTCGACAACAGCGACCCTCTCGCCGATGGCGCCGAACAGGCGGCCAGCGCG
CCCCAGGAGAGCCCTCTCCAGGAAAGCGCCACGCCCAGCGTCGAAAGCCTCGACGACGACCAGTGGAGCGAA
CGCATACCCAGCGAGTTGCCGGTGGATACCGCCTGGGAAGACATCTACCAGACCAGCGCCAGCAGCCTGCCC
AGCAACGACGATGACGAATGGGACTTCACCGCGCGCACCAGCAGCGGCGAGAGCCTGCACAGCCACCTGCTC
TGGCAGGTCAACCTGGCACCGATGTCGGACACCGATCGGATGATCGCGGTGACCATCATCGATAGCATCAAC
AACGATGGCTATCTCGAAGAGTCCCTCGAAGAAATCCTCGCCGCCATCGATCCGGAACTGGACGTCGAACTC
GACGAAGTGGAAGTCGTGCTGCGCCGCATCCAGCAACTGGAACCCGCCGGCATCGGCGCCCGCAACCTGCGC
GAGTGCCTGCTGCTGCAACTGCGCCAGTTGCCGTCCACCACGCCCTGGCTGAACGAAGCGCTGCGCCTGGTA
TCCGACTACCTCGACCTGCTCGGCGGCCGCGACTACAGCCAATTGATGCGGCGCATGAAGCTCAAGGAAGAC
GAACTGCGCCAGGTCATCGAGCTGATCCAGTGCCTGCATCCCCGGCCCGGTTCGCAGATCGAATCGAGCGAA
GCCGAATACATCGTCCCCGACGTCATTGTGCGCAAGGACAACGAGCGCTGGCTGGTCGAGCTGAACCAGGAG
GCGATGCCGCGCCTGCGCGTCAACGCCACCTACGCCGGCATGGTCCGCCGCGCCGACAGCAGCGCCGACAAT
ACCTTCATGCGCAACCAGTTGCAGGAAGCCCGCTGGTTCATCAAGAGCCTGCAGAGCCGCAACGAAACGCTG
ATGAAGGTCGCCACCCAGATCGTCGAGCACCAGCGCGGTTTCCTCGACTACGGCGAAGAAGCCATGAAGCCG
CTGGTCCTGCACGACATCGCCGAAGCGGTGGGCATGCACGAATCGACCATTTCGCGGGTCACCACGCAGAAA
TACATGCATACGCCGCGCGGCATTTTCGAGCTGAAATATTTCTTTTCAAGTCACGTCAGTACCGCTGAAGGC
GGGGAATGCTCGTCCACCGCGATCCGCGCGATCATCAAGAAACTGGTGGCCGCGGAAAATGCGAAAAAGCCA
TTGAGCGACAGCAAGATCGCTGGTTTACTGGAGGCACAGGGCATTCAAGTGGCTCGCCGCACCGTCGCCAAA
TACCGCGAATCCCTGGGCATAGCCCCTTCGAGCGAGCGCAAGCGACTGGTGTGA
Translation:
MKPSLVLKMGQQLTMTPQLQQAIRLLQLSTLDLQQEIQEALESNPMLERQEDGDDFDNSDPLADGAEQAASA
PQESPLQESATPSVESLDDDQWSERIPSELPVDTAWEDIYQTSASSLPSNDDDEWDFTARTSSGESLHSHLL
WQVNLAPMSDTDRMIAVTIIDSINNDGYLEESLEEILAAIDPELDVELDEVEVVLRRIQQLEPAGIGARNLR
ECLLLQLRQLPSTTPWLNEALRLVSDYLDLLGGRDYSQLMRRMKLKEDELRQVIELIQCLHPRPGSQIESSE
AEYIVPDVIVRKDNERWLVELNQEAMPRLRVNATYAGMVRRADSSADNTFMRNQLQEARWFIKSLQSRNETL
MKVATQIVEHQRGFLDYGEEAMKPLVLHDIAEAVGMHESTISRVTTQKYMHTPRGIFELKYFFSSHVSTAEG
GECSSTAIRAIIKKLVAAENAKKPLSDSKIAGLLEAQGIQVARRTVAKYRESLGIAPSSERKRLV*
AnnotationID:838GeneID:829
AnnotatorUID: diggins
Modification Date/Time: 2005-05-03 07:07:10
Gene Name:rpoN
Confidence Code:1
GeneProduct:RNA polymerase sigma-54 factor
Cell Localization:()
Synonyms:ntrA
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1508,pfam04963,pfam04552
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAQ17035.1| (AY341911) sigma factor RpoN [Pseudomonas fluorescens]
          Length = 497

 Score =  859 bits (2220), Expect = 0.0
 Identities = 429/497 (86%), Positives = 464/497 (93%)


>gb|AAN16366.1| (AF538690) sigma 54 [Pseudomonas alcaligenes]
          Length = 495

 Score =  857 bits (2214), Expect = 0.0
 Identities = 429/495 (86%), Positives = 460/495 (92%)






 
Structural Features:
COG1508, RpoN, DNA-directed RNA polymerase specialized sigma subunit, 
sigma54 homolog [Transcription]
CD-Length = 444 residues, 100.0% aligned
Score =  509 bits (1312), Expect = 6e-145
Identities = 248/498 (49%), Positives = 332/498 (66%), Gaps = 55/498 (11%)

pfam04963, Sigma54_CBD, Sigma-54 factor, core binding domain.
CD-Length = 195 residues, 100.0% aligned
Score =  262 bits (672), Expect = 1e-70
Identities = 113/202 (55%), Positives = 147/202 (72%), Gaps = 7/202 (3%)

pfam04552, Sigma54_DBD, Sigma-54, DNA binding domain.
CD-Length = 160 residues, 100.0% aligned
Score =  253 bits (647), Expect = 1e-67
Identities = 105/160 (65%), Positives = 130/160 (81%)






   
Genomic Context:






   
Comment:


















    ReferenceID:1661




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:18803




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31501




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:829_cdd.html


    		




 
URL:

















    ReferenceID:32847




  
Author/Investigator(s):
        Hendrickson EL, Plotnikova J, Mahajan-Miklos S, Rahme LG, Ausubel FM.





  
Title:
        Differential roles of the Pseudomonas aeruginosa PA14 rpoN gene in pathogenicity in plants, nematodes, insects, and mice.




  
PubMed:
        11717271


MedLine:
        




    
Source:
J Bacteriol. 2001 Dec;183(24):7126-34.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11717271

















    ReferenceID:32848




  
Author/Investigator(s):
        Yamano Y, Nishikawa T, Komatsu Y.





  
Title:
        Involvement of the RpoN protein in the transcription of the oprE gene in Pseudomonas aeruginosa.




  
PubMed:
        9595661


MedLine:
        




    
Source:
FEMS Microbiol Lett. 1998 May 1;162(1):31-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9595661

















    ReferenceID:32849




  
Author/Investigator(s):
        Jin S, Ishimoto K, Lory S.





  
Title:
        Nucleotide sequence of the rpoN gene and characterization of two downstream open reading frames in Pseudomonas aeruginosa.




  
PubMed:
        8113171


MedLine:
        




    
Source:
J Bacteriol. 1994 Mar;176(5):1316-22.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8113171

















    ReferenceID:32850




  
Author/Investigator(s):
        Farinha MA, Ronald SL, Kropinski AM, Paranchych W.





  
Title:
        Localization of the virulence-associated genes pilA, pilR, rpoN, fliA, fliC, ent, and fbp on the physical map of Pseudomonas aeruginosa PAO1 by pulsed-field electrophoresis.




  
PubMed:
        8454366


MedLine:
        




    
Source:
Infect Immun. 1993 Apr;61(4):1571-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8454366

















    ReferenceID:32851




  
Author/Investigator(s):
        Totten PA, Lara JC, Lory S.





  
Title:
        The rpoN gene product of Pseudomonas aeruginosa is required for expression of diverse genes, including the flagellin gene.




  
PubMed:
        2152909


MedLine:
        




    
Source:
J Bacteriol. 1990 Jan;172(1):389-96.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2152909

















    ReferenceID:32852




  
Author/Investigator(s):
        Ishimoto KS, Lory S.





  
Title:
        Formation of pilin in Pseudomonas aeruginosa requires the alternative sigma factor (RpoN) of RNA polymerase.




  
PubMed:
        2564676


MedLine:
        




    
Source:
Proc Natl Acad Sci U S A. 1989 Mar;86(6):1954-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2564676









           
Homologs By Global Alignment 

           

       



     
Gene ID:829
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
1499
                           PA4462_tr
                           translation of PA4462
                           497
                           99.99
                           99.99
                           0
                           2507.0
     

     
     
54382
                           gb|AAG07850.1|AE004860_6
                           (AE004860) RNA polymerase sigma-54 factor [Pseudomonas aeruginosa PAO1]
                           497
                           99.99
                           99.99
                           0
                           2507.0
     

     
     
54383
                           gb|AAA19793.1|
                           (L26916) rpoN [Pseudomonas aeruginosa]
                           497
                           99.79
                           99.99
                           0
                           2504.0
     

     
     
54387
                           gb|AAN66577.1|AE016286_1
                           (AE016777) RNA polymerase sigma-54 factor [Pseudomonas putida KT2440]
                           498
                           86.34
                           93.77
                           2
                           2204.0
     

     
     
54388
                           gb|AAA88444.1|
                           (M24916) sigma factor [Pseudomonas putida]
                           498
                           86.34
                           93.77
                           2
                           2204.0
     

     






      

          
GC ORFID: 43831How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4462Glimmer Score: 

          
Start: 4420140Stop: 4421633

          
Length: 1494


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4462 translation of PA4462Homolog Bit Score 970.0

          
Other Homologs:  t_PA4462 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAAACCATCGCTAGTCCTCAAGATGGGCCAGCAGCTGACGATGACGCCGCAGCTGCAACAGGCCATACGC 
CTCCTCCAGCTATCCACCCTGGACCTCCAGCAGGAAATCCAGGAAGCGCTGGAATCCAATCCCATGCTCGAA 
CGCCAGGAAGACGGCGACGATTTCGACAACAGCGACCCTCTCGCCGATGGCGCCGAACAGGCGGCCAGCGCG 
CCCCAGGAGAGCCCTCTCCAGGAAAGCGCCACGCCCAGCGTCGAAAGCCTCGACGACGACCAGTGGAGCGAA 
CGCATACCCAGCGAGTTGCCGGTGGATACCGCCTGGGAAGACATCTACCAGACCAGCGCCAGCAGCCTGCCC 
AGCAACGACGATGACGAATGGGACTTCACCGCGCGCACCAGCAGCGGCGAGAGCCTGCACAGCCACCTGCTC 
TGGCAGGTCAACCTGGCACCGATGTCGGACACCGATCGGATGATCGCGGTGACCATCATCGATAGCATCAAC 
AACGATGGCTATCTCGAAGAGTCCCTCGAAGAAATCCTCGCCGCCATCGATCCGGAACTGGACGTCGAACTC 
GACGAAGTGGAAGTCGTGCTGCGCCGCATCCAGCAACTGGAACCCGCCGGCATCGGCGCCCGCAACCTGCGC 
GAGTGCCTGCTGCTGCAACTGCGCCAGTTGCCGTCCACCACGCCCTGGCTGAACGAAGCGCTGCGCCTGGTA 
TCCGACTACCTCGACCTGCTCGGCGGCCGCGACTACAGCCAATTGATGCGGCGCATGAAGCTCAAGGAAGAC 
GAACTGCGCCAGGTCATCGAGCTGATCCAGTGCCTGCATCCCCGGCCCGGTTCGCAGATCGAATCGAGCGAA 
GCCGAATACATCGTCCCCGACGTCATTGTGCGCAAGGACAACGAGCGCTGGCTGGTCGAGCTGAACCAGGAG 
GCGATGCCGCGCCTGCGCGTCAACGCCACCTACGCCGGCATGGTCCGCCGCGCCGACAGCAGCGCCGACAAT 
ACCTTCATGCGCAACCAGTTGCAGGAAGCCCGCTGGTTCATCAAGAGCCTGCAGAGCCGCAACGAAACGCTG 
ATGAAGGTCGCCACCCAGATCGTCGAGCACCAGCGCGGTTTCCTCGACTACGGCGAAGAAGCCATGAAGCCG 
CTGGTCCTGCACGACATCGCCGAAGCGGTGGGCATGCACGAATCGACCATTTCGCGGGTCACCACGCAGAAA 
TACATGCATACGCCGCGCGGCATTTTCGAGCTGAAATATTTCTTTTCAAGTCACGTCAGTACCGCTGAAGGC 
GGGGAATGCTCGTCCACCGCGATCCGCGCGATCATCAAGAAACTGGTGGCCGCGGAAAATGCGAAAAAGCCA 
TTGAGCGACAGCAAGATCGCTGGTTTACTGGAGGCACAGGGCATTCAAGTGGCTCGCCGCACCGTCGCCAAA 
TACCGCGAATCCCTGGGCATAGCCCCTTCGAGCGAGCGCAAGCGACTGGTGTGA