ViewGene
Locus Name:
GeneID:
Location:

GeneID:3229
TrivialName: PA14_19120
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_19120
PAO1 Ortholog Locus:PA3477
Sequence Length:726
Protein Length:241
Start: 1650990
Stop: 1651715
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG06865.1|AE004768_10 (AE004768) transcriptional regulator RhlR [Pseudomonas aeruginosa PAO1]
Identities = 241/241 (100%), Positives = 241/241 (100%)
Sequence:
ATGAGGAATGACGGAGGCTTTTTGCTGTGGTGGGACGGTTTGCGTAGCGAGATGCAGCCGATCCACGACAGC
CAGGGCGTGTTCGCCGTCCTGGAAAAGGAAGTGCGGCGCCTGGGCTTCGATTACTACGCCTATGGCGTGCGC
CACACGATTCCCTTCACCCGGCCGAAGACCGAGGTCCATGGCACCTATCCCAAGGCCTGGCTGGAGCGATAC
CAGATGCAGAACTACGGGGCCGTGGATCCGGCGATCCTCAACGGCCTGCGCTCCTCGGAAATGGTGGTCTGG
AGCGACAGCCTGTTCGACCAGAGCCGGATGCTCTGGAACGAGGCTCGCGATTGGGGCCTCTGTGTCGGCGCG
ACCCTGCCGATCCGCGCGCCGAACAATTTGCTCAGCGTGCTTTCCGTGGCGCGCGACCAGCAGAACATCTCC
AGCTTCGAGCGCGAGGAAATCCGCCTGCGGCTGCGTTGCATGATCGAGTTGCTGACCCAGAAGCTGACCGAC
CTGGAGCATCCGATGCTGATGTCCAACCCGGTCTGCCTGAGCCATCGCGAACGCGAGATCCTGCAATGGACC
GCCGACGGCAAGAGTTCCGGGGAAATCGCCATCATCCTGAGCATCTCCGAGAGCACGGTGAACTTCCACCAC
AAGAACATCCAGAAGAAGTTCGACGCGCCGAACAAGACGCTGGCTGCCGCCTACGCCGCGGCGCTGGGCCTC
ATCTGA
Translation:
MRNDGGFLLWWDGLRSEMQPIHDSQGVFAVLEKEVRRLGFDYYAYGVRHTIPFTRPKTEVHGTYPKAWLERY
QMQNYGAVDPAILNGLRSSEMVVWSDSLFDQSRMLWNEARDWGLCVGATLPIRAPNNLLSVLSVARDQQNIS
SFEREEIRLRLRCMIELLTQKLTDLEHPMLMSNPVCLSHREREILQWTADGKSSGEIAIILSISESTVNFHH
KNIQKKFDAPNKTLAAAYAAALGLI*
AnnotationID:3237GeneID:3229
AnnotatorUID: diggins
Modification Date/Time: 2005-04-19 10:10:51
Gene Name:rhlR
Confidence Code:1
GeneProduct:acylhomoserine lactone dependent transcriptional regulator
Cell Localization:()
Synonyms:sdiA
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:transcriptional regulator of ftsQAZ gene cluster
Functional Category Confidence Code:5
COGs:pfam03472
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAK73190.1| (AY040629) transcriptional activator CsaR [Pseudomonas
           chlororaphis]
          Length = 241

 Score =  324 bits (831), Expect = 2e-88
 Identities = 161/235 (68%), Positives = 191/235 (81%)

>gb|AAL20862.1| (AE008786) transcriptional regulator of ftsQAZ gene cluster
           [Salmonella typhimurium LT2]
          Length = 240

 Score =  207 bits (528), Expect = 3e-53
 Identities = 107/238 (44%), Positives = 146/238 (61%)

>dbj|BAA15736.1| (D90832) SdiA regulatory protein. [Escherichia coli]
          Length = 240

 Score =  187 bits (476), Expect = 4e-47
 Identities = 97/238 (40%), Positives = 144/238 (60%)








 
Structural Features:
pfam03472, Autoind_bind, Autoinducer binding domain. 
This domain is found a a large family of transcriptional regulators. 
CD-Length = 150 residues, 100.0% aligned
Score =  143 bits (363), Expect = 1e-35
Identities = 63/150 (42%), Positives = 88/150 (58%), Gaps = 4/150 (2%)







   
Genomic Context:






   
Comment:


















    ReferenceID:6461




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:23603




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:32082




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3229_cdd.html


    		




 
URL:

















    ReferenceID:34091




  
Author/Investigator(s):
        Ochsner UA, Koch AK, Fiechter A, Reiser J.





  
Title:
        Isolation and characterization of a regulatory gene affecting rhamnolipid biosurfactant synthesis in Pseudomonas aeruginosa.




  
PubMed:
        8144472


MedLine:
        




    
Source:
J Bacteriol. 1994 Apr;176(7):2044-54.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8144472

















    ReferenceID:34092




  
Author/Investigator(s):
        Lamb JR, Patel H, Montminy T, Wagner VE, Iglewski BH.





  
Title:
        Functional domains of the RhlR transcriptional regulator of Pseudomonas aeruginosa.




  
PubMed:
        14645272


MedLine:
        




    
Source:
J Bacteriol. 2003 Dec;185(24):7129-39.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14645272

















    ReferenceID:34093




  
Author/Investigator(s):
        Medina G, Juarez K, Diaz R, Soberon-Chavez G.





  
Title:
        Transcriptional regulation of Pseudomonas aeruginosa rhlR, encoding a quorum-sensing regulatory protein.




  
PubMed:
        14600219


MedLine:
        




    
Source:
Microbiology. 2003 Nov;149(Pt 11):3073-81.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14600219

















    ReferenceID:34094




  
Author/Investigator(s):
        Medina G, Juarez K, Valderrama B, Soberon-Chavez G.





  
Title:
        Mechanism of Pseudomonas aeruginosa RhlR transcriptional regulation of the rhlAB promoter.




  
PubMed:
        14526008


MedLine:
        




    
Source:
J Bacteriol. 2003 Oct;185(20):5976-83.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14526008









           
Homologs By Global Alignment 

           

       



     
Gene ID:3229
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
5200
                           PA3477_tr
                           translation of PA3477
                           241
                           99.99
                           99.99
                           0
                           1268.0
     

     
     
145967
                           gb|AAG06865.1|AE004768_10
                           (AE004768) transcriptional regulator RhlR [Pseudomonas aeruginosa PAO1]
                           241
                           99.99
                           99.99
                           0
                           1268.0
     

     
     
145968
                           gb|AAC44036.1|
                           (U40458) RhlR [Pseudomonas aeruginosa]
                           241
                           99.99
                           99.99
                           0
                           1268.0
     

     
     
145969
                           gb|AAA62130.1|
                           (L28170) regulatory protein [Pseudomonas aeruginosa]
                           241
                           99.99
                           99.99
                           0
                           1268.0
     

     
     
145970
                           gb|AAA25983.1|
                           (L08962) rhlR [Pseudomonas aeruginosa]
                           241
                           99.99
                           99.99
                           0
                           1268.0
     

     






      

          
GC ORFID: 46231How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3477Glimmer Score: 

          
Start: 3302943Stop: 3302218

          
Length: 726


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3477 translation of PA3477Homolog Bit Score 493.0

          
Other Homologs:  t_PA3477 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGGAATGACGGAGGCTTTTTGCTGTGGTGGGACGGTTTGCGTAGCGAGATGCAGCCGATCCACGACAGC 
CAGGGCGTGTTCGCCGTCCTGGAAAAGGAAGTGCGGCGCCTGGGCTTCGATTACTACGCCTATGGCGTGCGC 
CACACGATTCCCTTCACCCGGCCGAAGACCGAGGTCCATGGCACCTATCCCAAGGCCTGGCTGGAGCGATAC 
CAGATGCAGAACTACGGGGCCGTGGATCCGGCGATCCTCAACGGCCTGCGCTCCTCGGAAATGGTGGTCTGG 
AGCGACAGCCTGTTCGACCAGAGCCGGATGCTCTGGAACGAGGCTCGCGATTGGGGCCTCTGTGTCGGCGCG 
ACCCTGCCGATCCGCGCGCCGAACAATTTGCTCAGCGTGCTTTCCGTGGCGCGCGACCAGCAGAACATCTCC 
AGCTTCGAGCGCGAGGAAATCCGCCTGCGGCTGCGTTGCATGATCGAGTTGCTGACCCAGAAGCTGACCGAC 
CTGGAGCATCCGATGCTGATGTCCAACCCGGTCTGCCTGAGCCATCGCGAACGCGAGATCCTGCAATGGACC 
GCCGACGGCAAGAGTTCCGGGGAAATCGCCATCATCCTGAGCATCTCCGAGAGCACGGTGAACTTCCACCAC 
AAGAACATCCAGAAGAAGTTCGACGCGCCGAACAAGACGCTGGCTGCCGCCTACGCCGCGGCGCTGGGCCTC 
ATCTGA