ViewGene
Locus Name:
GeneID:
Location:

GeneID:2247
TrivialName: PA14_32060
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_32060
PAO1 Ortholog Locus:PA2519
Sequence Length:957
Protein Length:318
Start: 2790219
Stop: 2791175
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05907.1|AE004679_1 (AE004679) transcriptional regulator XylS [Pseudomonas aeruginosa PAO1]
Identities = 317/318 (99%), Positives = 317/318 (99%)
Sequence:
ATGAATGCCTCCTTGCTCAGCGAGCGCAGCCGGGTGTTCGAACGTGCCGACCCCTATGCGGTGTCCGGCTAC
GTCAACCGGCACGTTGGTACGCACTGCATACGCCTGCCGGCCGCCGGCAGGCCGCAAGCCAGCCTCGACCAC
CGCACCTTCGCCAGCCTCGACCTGTGCCGGATCAGCTACGGCGCGGCGGTACGGGTCACCTCGCCGGCGCTG
GAGAGCATCTTCCACCTGCAGATCCTCCTGCGCGGCCACTGCCTGTGGTGCGGCGGCGGGCAGGAACACGCC
CTGGCGCCGGGCGAGCTGTTGCTGATCAACCCGGACGATCCGGTCGACCTGACCTATTCGGCGGACTGCGAG
AAATTCATCGTCAAGCTGCCCTGCGCGCTGCTCGaAGCGATCTGCGCCGAGCAGCGCTGGAGCCATCCGGCA
CGCGGCGTGCGTTTCCTCGAGCATCGCTATCGCCTGGACCAGCTGGAAGGCTTCGTCGGCCTGCTCGCCCTG
GTCTGCCGCGAGGCCGAGTCCGGCGAGCGGCTGGCGCGGGTCGACAGCCACTTCGAGCAGATCCTCGGCAGC
AAGCTGCTGACCCTGCTGAAGACCAACGTCAGCCGCGAGGACCCCGGCGATGCGCAGGTCGTCTTCGCCCGC
CTCGATGCCTACATCCGCCGCCATCTGCAGAGCGAGATCGAGGTCGCGGCGCTGGCCGAGCAGGCGCACATG
AGCACTCGCTCGCTGTACGCGCTGTTCGAGCGCCAGCTTGGCGAGAGCCCTCGGCAATACATTCGCCGGCTG
CGCCTGGAGCGCATCCGCGCCTGCCTGGAAGACCCCGGCTGCCGGGTACGCAACCTCACCGAACTGGCCCTG
GACTTCGGTTTCGCCCACCTCGGCCGCTTCGCCGAGCAATATCGCCGGCAGTTCGGCGAGCTGCCTTCGGAA
ACCCTGCGCCGGCGCGCCTAG
Translation:
MNASLLSERSRVFERADPYAVSGYVNRHVGTHCIRLPAAGRPQASLDHRTFASLDLCRISYGAAVRVTSPAL
ESIFHLQILLRGHCLWCGGGQEHALAPGELLLINPDDPVDLTYSADCEKFIVKLPCALLEAICAEQRWSHPA
RGVRFLEHRYRLDQLEGFVGLLALVCREAESGERLARVDSHFEQILGSKLLTLLKTNVSREDPGDAQVVFAR
LDAYIRRHLQSEIEVAALAEQAHMSTRSLYALFERQLGESPRQYIRRLRLERIRACLEDPGCRVRNLTELAL
DFGFAHLGRFAEQYRRQFGELPSETLRRRA*
AnnotationID:2255GeneID:2247
AnnotatorUID: diggins
Modification Date/Time: 2005-03-06 18:06:51
Gene Name:xylS
Confidence Code:2
GeneProduct:transcriptional regulator XylS
Cell Localization:()
Synonyms:benR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:benABC operon transcriptional activator BenR
Functional Category Confidence Code:5
COGs:smart00342,COG2207
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAK52286.1| (AY026914) transcriptional regulatory protein BenM [Pseudomonas
           putida]
          Length = 318

 Score =  634 bits (1634), Expect = 0.0
 Identities = 317/318 (99%), Positives = 317/318 (99%)

>gb|AAN68767.1|AE016508_8 (AE016785) benABC operon transcriptional activator BenR
           [Pseudomonas putida KT2440]
          Length = 318

 Score =  412 bits (1059), Expect = e-114
 Identities = 202/318 (63%), Positives = 242/318 (76%)

>dbj|BAB21583.1| (AB035324) transcriptional activator [Burkholderia sp. TH2]
          Length = 321

 Score =  260 bits (664), Expect = 9e-69
 Identities = 145/315 (46%), Positives = 196/315 (62%), Gaps = 9/315 (2%)








 
Structural Features:
smart00342, HTH_ARAC, helix_turn_helix, arabinose operon control protein
CD-Length = 84 residues, 100.0% aligned
Score = 73.7 bits (181), Expect = 3e-14
Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 3/87 (3%)

COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]
CD-Length = 127 residues,  94.5% aligned
Score = 71.1 bits (173), Expect = 2e-13
Identities = 42/123 (34%), Positives = 64/123 (52%), Gaps = 3/123 (2%)







   
Genomic Context:






   
Comment:


















    ReferenceID:4497




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21643




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:33076




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2247_cdd.html


    		




 
URL:

















    ReferenceID:34519




  
Author/Investigator(s):
        Cowles CE, Nichols NN, Harwood CS.





  
Title:
        BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida.




  
PubMed:
        11053377


MedLine:
        




    
Source:
J Bacteriol. 2000 Nov;182(22):6339-46.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11053377

















    ReferenceID:34520




  
Author/Investigator(s):
        Zhang C, Huang M, Holloway BW.





  
Title:
        Mapping of ben genes of Pseudomonas aeruginosa.




  
PubMed:
        8224789


MedLine:
        




    
Source:
FEMS Microbiol Lett. 1993 Sep 15;112(3):255-9.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8224789

















    ReferenceID:34521




  
Author/Investigator(s):
        Jeffrey WH, Cuskey SM, Chapman PJ, Resnick S, Olsen RH.





  
Title:
        Characterization of Pseudomonas putida mutants unable to catabolize benzoate: cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TO




  
PubMed:
        1629155


MedLine:
        




    
Source:
 Bacteriol. 1992 Aug;174(15):4986-96.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1629155

















    ReferenceID:34522




  
Author/Investigator(s):
        Mermod N, Ramos JL, Bairoch A, Timmis KN.





  
Title:
        The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon.




  
PubMed:
        3475526


MedLine:
        




    
Source:
Mol Gen Genet. 1987 May;207(2-3):349-54.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3475526

















    ReferenceID:34523




  
Author/Investigator(s):
        Spooner RA, Lindsay K, Franklin FC.





  
Title:
        Genetic, functional and sequence analysis of the xylR and xylS regulatory genes of the TOL plasmid pWW0.




  
PubMed:
        2430049


MedLine:
        




    
Source:
J Gen Microbiol. 1986 May;132 ( Pt 5):1347-58.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2430049

















    ReferenceID:34524




  
Author/Investigator(s):
        Inouye S, Nakazawa A, Nakazawa T.





  
Title:
        Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein product.




  
PubMed:
        3023186


MedLine:
        




    
Source:
Gene. 1986;44(2-3):235-42.

Erratum in:
    * Gene 1986;45(3):339.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3023186









           
Homologs By Global Alignment 

           

       



     
Gene ID:2247
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3807
                           PA2519_tr
                           translation of PA2519
                           318
                           99.68
                           99.68
                           0
                           1634.0
     

     
     
117139
                           gb|AAG05907.1|AE004679_1
                           (AE004679) transcriptional regulator XylS [Pseudomonas aeruginosa PAO1]
                           318
                           99.68
                           99.68
                           0
                           1634.0
     

     
     
117140
                           gb|AAK52286.1|
                           (AY026914) transcriptional regulatory protein BenM [Pseudomonas putida]
                           318
                           99.68
                           99.68
                           0
                           1634.0
     

     
     
117141
                           emb|CAB56472.1|
                           (Y14018) hypothetical protein [Pseudomonas aeruginosa]
                           318
                           99.37
                           99.37
                           0
                           1629.0
     

     
     
117143
                           gb|AAF63447.1|AF218267_4
                           (AF218267) BenR [Pseudomonas putida]
                           318
                           63.52
                           75.15
                           0
                           1055.0
     

     






      

          
GC ORFID: 45249How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA2519Glimmer Score: 

          
Start: 2163705Stop: 2162749

          
Length: 957


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_PA2519 translation of PA2519Homolog Bit Score 634.0

          
Other Homologs:  t_PA2519 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAATGCCTCCTTGCTCAGCGAGCGCAGCCGGGTGTTCGAACGTGCCGACCCCTATGCGGTGTCCGGCTAC 
GTCAACCGGCACGTTGGTACGCACTGCATACGCCTGCCGGCCGCCGGCAGGCCGCAAGCCAGCCTCGACCAC 
CGCACCTTCGCCAGCCTCGACCTGTGCCGGATCAGCTACGGCGCGGCGGTACGGGTCACCTCGCCGGCGCTG 
GAGAGCATCTTCCACCTGCAGATCCTCCTGCGCGGCCACTGCCTGTGGTGCGGCGGCGGGCAGGAACACGCC 
CTGGCGCCGGGCGAGCTGTTGCTGATCAACCCGGACGATCCGGTCGACCTGACCTATTCGGCGGACTGCGAG 
AAATTCATCGTCAAGCTGCCCTGCGCGCTGCTCGaAGCGATCTGCGCCGAGCAGCGCTGGAGCCATCCGGCA 
CGCGGCGTGCGTTTCCTCGAGCATCGCTATCGCCTGGACCAGCTGGAAGGCTTCGTCGGCCTGCTCGCCCTG 
GTCTGCCGCGAGGCCGAGTCCGGCGAGCGGCTGGCGCGGGTCGACAGCCACTTCGAGCAGATCCTCGGCAGC 
AAGCTGCTGACCCTGCTGAAGACCAACGTCAGCCGCGAGGACCCCGGCGATGCGCAGGTCGTCTTCGCCCGC 
CTCGATGCCTACATCCGCCGCCATCTGCAGAGCGAGATCGAGGTCGCGGCGCTGGCCGAGCAGGCGCACATG 
AGCACTCGCTCGCTGTACGCGCTGTTCGAGCGCCAGCTTGGCGAGAGCCCTCGGCAATACATTCGCCGGCTG 
CGCCTGGAGCGCATCCGCGCCTGCCTGGAAGACCCCGGCTGCCGGGTACGCAACCTCACCGAACTGGCCCTG 
GACTTCGGTTTCGCCCACCTCGGCCGCTTCGCCGAGCAATATCGCCGGCAGTTCGGCGAGCTGCCTTCGGAA 
ACCCTGCGCCGGCGCGCCTAG