ViewGene
Locus Name:
GeneID:
Location:

GeneID:2108
TrivialName: PA14_17480
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_17480
PAO1 Ortholog Locus:PA3622
Sequence Length:1005
Protein Length:334
Start: 1499097
Stop: 1500101
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG07010.1|AE004782_8 (AE004782) sigma factor RpoS [Pseudomonas aeruginosa PAO1]
Identities = 334/334 (100%), Positives = 334/334 (100%)
Sequence:
ATGGCACTCAAAAAAGAAGGGCCGGAGTTTGACCACGATGATGAAGTGCTCCTCCTGGAGCCCGGCATCATG
CTGGACGAGTCGTCTGCCGACGAGCAGCCTTCTCCCCGGGCAACTCCAAAAGCCACCACTTCCTTCTCTTCC
AAACAACACAAGCACATCGACTACACGCGCGCGTTGGACGCAACGCAGCTGTATCTCAACGAAATCGGTTTC
TCGCCCCTGTTGACGCCCGAAGAGGAAGTCCACTTCGCTCGTCTGGCGCAGAAGGGCGATCCCGCTGGTCGG
AAGCGGATGATCGAGAGCAACCTGCGGTTGGTGGTGAAGATCGCCCGGCGCTATGTCAATCGCGGACTGTCC
CTGCTCGACCTGATCGAGGAAGGCAACCTAGGCCTGATCCGCGCCGTGGAGAAGTTCGATCCGGAGCGCGGA
TTCCGGTTCTCGACCTACGCCACCTGGTGGATCCGCCAGACCATCGAACGGGCCATCATGAACCAGACCCGG
ACCATTCGCTTGCCGATCCATGTGGTCAAGGAGCTCAACGTCTACCTGCGTGCGGCGCGGGAACTGACCCAC
AAGCTCGACCACGAACCTTCACCCGAAGAAATCGCCAACCTGCTGGAGAAGCCGGTCGCCGAGGTCAAGCGC
ATGCTCGGCCTGAACGAACGGGTGACTTCGGTAGACGTCTCTCTTGGTCCGGACTCGGACAAGACCCTGCTG
GATACGCTCACCGACGATCGCCCCACCGATCCGTGCGAGCTGCTGCAGGATGACGATCTCAGCGAAAGCATC
GACCAGTGGCTGACGGAACTCACCGACAAGCAGCGTGAGGTGGTGATTCGCCGCTTCGGCTTGCGCGGGCAC
GAAAGCAGCACGCTGGAAGAGGTCGGTCAGGAAATCGGCCTGACCCGCGAGCGGGTTCGTCAGATCCAGGTC
GAGGCGCTGAAGCGCCTGCGGGAGATCCTGGAGAAGAACGGCCTGTCGAGTGACGCGCTGTTCCAGTGA
Translation:
MALKKEGPEFDHDDEVLLLEPGIMLDESSADEQPSPRATPKATTSFSSKQHKHIDYTRALDATQLYLNEIGF
SPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERG
FRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKR
MLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGH
ESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDALFQ*
AnnotationID:2116GeneID:2108
AnnotatorUID: diggins
Modification Date/Time: 2005-04-20 18:06:24
Gene Name:rpoS
Confidence Code:1
GeneProduct:sigma factor RpoS
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:RNA polymerase principal sigma factor
Functional Category Confidence Code:5
COGs:COG0568
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO55085.1| (AE016861) RNA polymerase sigma-38 factor [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 335

 Score =  578 bits (1490), Expect = e-164
 Identities = 297/335 (88%), Positives = 314/335 (93%), Gaps = 1/335 (0%)

>gb|AAK29754.1| (AY029155) stationary phase sigma factor RpoS [Azotobacter
           vinelandii]
          Length = 238

 Score =  447 bits (1149), Expect = e-125
 Identities = 225/238 (94%), Positives = 231/238 (97%)

>gb|AAG53883.1|AF275947_2 (AF275947) sigma factor RpoS [Escherichia coli]
          Length = 366

 Score =  416 bits (1069), Expect = e-115
 Identities = 219/329 (66%), Positives = 255/329 (77%), Gaps = 12/329 (3%)






 
Structural Features:
COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) 
[Transcription]
CD-Length = 342 residues,  97.7% aligned
Score =  292 bits (748), Expect = 9e-80
Identities = 139/334 (41%), Positives = 195/334 (58%), Gaps = 11/334 (3%)






   
Genomic Context:






   
Comment:


















    ReferenceID:4219




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:21365




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:31920




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:2108_cdd.html


    		




 
URL:

















    ReferenceID:34178




  
Author/Investigator(s):
        Tanaka K, Takahashi H.





  
Title:
        Cloning, analysis and expression of an rpoS homologue gene from Pseudomonas aeruginosa PAO1.




  
PubMed:
        7959068


MedLine:
        




    
Source:
Gene. 1994 Dec 2;150(1):81-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7959068

















    ReferenceID:34179




  
Author/Investigator(s):
        Schuster M, Hawkins AC, Harwood CS, Greenberg EP.





  
Title:
        The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing.




  
PubMed:
        14763974


MedLine:
        




    
Source:
Mol Microbiol. 2004 Feb;51(4):973-85.






    
Reference Type:Journal 







    
Data:


    		




 
URL:Mol Microbiol. 2004 Feb;51(4):973-85.









           
Homologs By Global Alignment 

           

       



     
Gene ID:2108
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
3613
                           PA3622_tr
                           translation of PA3622
                           334
                           99.99
                           99.99
                           0
                           1695.0
     

     
     
111309
                           gb|AAG07010.1|AE004782_8
                           (AE004782) sigma factor RpoS [Pseudomonas aeruginosa PAO1]
                           334
                           99.99
                           99.99
                           0
                           1695.0
     

     
     
111310
                           dbj|BAA05131.1|
                           (D26134) RNA polymerase principal sigma factor [Pseudomonas aeruginosa]
                           334
                           99.99
                           99.99
                           0
                           1695.0
     

     
     
111311
                           gb|AAO55085.1|
                           (AE016861) RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato str. DC3000]
                           335
                           88.65
                           93.73
                           1
                           1492.0
     

     
     
111312
                           gb|AAC16326.1|
                           (AF061853) sigma factor; RpoS [Pseudomonas syringae pv. tomato]
                           335
                           88.65
                           93.73
                           1
                           1492.0
     

     






      

          
GC ORFID: 45110How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA3622Glimmer Score: 

          
Start: 3454840Stop: 3453836

          
Length: 1005


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA3622 translation of PA3622Homolog Bit Score 657.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4653 (ORF: BLASTX 576.0), t_PA3622 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCACTCAAAAAAGAAGGGCCGGAGTTTGACCACGATGATGAAGTGCTCCTCCTGGAGCCCGGCATCATG 
CTGGACGAGTCGTCTGCCGACGAGCAGCCTTCTCCCCGGGCAACTCCAAAAGCCACCACTTCCTTCTCTTCC 
AAACAACACAAGCACATCGACTACACGCGCGCGTTGGACGCAACGCAGCTGTATCTCAACGAAATCGGTTTC 
TCGCCCCTGTTGACGCCCGAAGAGGAAGTCCACTTCGCTCGTCTGGCGCAGAAGGGCGATCCCGCTGGTCGG 
AAGCGGATGATCGAGAGCAACCTGCGGTTGGTGGTGAAGATCGCCCGGCGCTATGTCAATCGCGGACTGTCC 
CTGCTCGACCTGATCGAGGAAGGCAACCTAGGCCTGATCCGCGCCGTGGAGAAGTTCGATCCGGAGCGCGGA 
TTCCGGTTCTCGACCTACGCCACCTGGTGGATCCGCCAGACCATCGAACGGGCCATCATGAACCAGACCCGG 
ACCATTCGCTTGCCGATCCATGTGGTCAAGGAGCTCAACGTCTACCTGCGTGCGGCGCGGGAACTGACCCAC 
AAGCTCGACCACGAACCTTCACCCGAAGAAATCGCCAACCTGCTGGAGAAGCCGGTCGCCGAGGTCAAGCGC 
ATGCTCGGCCTGAACGAACGGGTGACTTCGGTAGACGTCTCTCTTGGTCCGGACTCGGACAAGACCCTGCTG 
GATACGCTCACCGACGATCGCCCCACCGATCCGTGCGAGCTGCTGCAGGATGACGATCTCAGCGAAAGCATC 
GACCAGTGGCTGACGGAACTCACCGACAAGCAGCGTGAGGTGGTGATTCGCCGCTTCGGCTTGCGCGGGCAC 
GAAAGCAGCACGCTGGAAGAGGTCGGTCAGGAAATCGGCCTGACCCGCGAGCGGGTTCGTCAGATCCAGGTC 
GAGGCGCTGAAGCGCCTGCGGGAGATCCTGGAGAAGAACGGCCTGTCGAGTGACGCGCTGTTCCAGTGA