ViewGene
Locus Name:
GeneID:
Location:

GeneID:6616
TrivialName: PA14_09110
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09110
PAO1 Ortholog Locus:
Sequence Length:288
Protein Length:95
Start: 771395
Stop: 771681
Strand: +
Type:
ChromosomeID:2
Status: INACTIVE
Frame Discrepancy: TRUE
Missense Discrepancy:TRUE
Comments:
Inactivated and Replaced by GeneID 7355. Homology: gb|AAG07626.1|AE004841_4 (AE004841) DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa PAO1]
Identities = 86/86 (100%), Positives = 86/86 (100%)
Sequence:
ATGCAGAGTTCGGTAAATGAGTTCCTGACCCCCCGCCACATCGATGTGCAGGTGGTCAGTCAAACCCGCGCC
AAGATCACGCTCGAGCCTCTCGAGCGTGGTTTTGGTCACACCCTGGGCAACGCGCTGCGTCGCATCCTGTTG
TCCTCCATGCCTGGCTGCGCAGTGGTCGAGGCCGAGATCGACGGCGTACTCCACGAGTACTCGGCGATCGAA
GGTGTGCAGGAAGATGTAATCGAGATCCTGCTGAACCTGAAaaggTCTGGCCATCAAGCTGCACGGTCGTGA
Translation:
MQSSVNEFLTPRHIDVQVVSQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVVEAEIDGVLHEYSAIE
GVQEDVIEILLNLKRSGHQAARS*
AnnotationID:6617GeneID:6616
AnnotatorUID: danlee
Modification Date/Time: 2006-02-01 18:06:20
Gene Name:
Confidence Code:4
GeneProduct:
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:()
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:
Secondary Functional Category(ies):
EC Number:
Status:INACTIVE
Pathway:






 
Homology:
>gb|AAO54193.1| (AE016858) DNA-directed RNA polymerase, alpha subunit
          [Pseudomonas syringae pv. tomato str. DC3000]
          Length = 333

 Score =  164 bits (415), Expect = 1e-40
 Identities = 84/86 (97%), Positives = 84/86 (97%)

>gb|AAN66109.1|AE016239_4 (AE016775) DNA-directed RNA polymerase, alpha subunit
          [Pseudomonas putida KT2440]
          Length = 333

 Score =  164 bits (415), Expect = 1e-40
 Identities = 84/86 (97%), Positives = 84/86 (97%)

>dbj|BAA11840.1| (D83194) RNA polymerase alpha subunit [Shewanella sp.]
          Length = 328

 Score =  146 bits (369), Expect = 2e-35
 Identities = 71/86 (82%), Positives = 78/86 (90%)








 
Structural Features:






   
Genomic Context:






   
Comment:


















    ReferenceID:13007




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:30329




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36624




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:6616_cdd.html


    		




 
URL:

















    ReferenceID:36701




  
Author/Investigator(s):
        Ma JF, Ochsner UA, Klotz MG, Nanayakkara VK, Howell ML, Johnson Z, Posey JE, Vasil ML, Monaco JJ, Hassett DJ.





  
Title:
        Bacterioferritin A modulates catalase A (KatA) activity and resistance to hydrogen peroxide in Pseudomonas aeruginosa.




  
PubMed:
        10368148


MedLine:
        




    
Source:
J Bacteriol. 1999 Jun;181(12):3730-42.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10368148

















    ReferenceID:36704




  
Author/Investigator(s):
        Meek DW, Hayward RS.





  
Title:
        Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?




  
PubMed:
        6379605


MedLine:
        




    
Source:
Nucleic Acids Res. 1984 Jul 25;12(14):5813-21.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=6379605









           
Homologs By Global Alignment 

           

       



     
Gene ID:6616
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
200317
                           gb|AAC05400.1|
                           (M74510) RNA polymerase alpha subunit [Buchnera aphidicola]
                           113
                           54.86
                           65.48
                           18
                           314.0
     

     
     
200292
                           emb|CAA23646.1|
                           (V00353) unnamed protein product [Escherichia coli]
                           162
                           43.82
                           47.53
                           70
                           348.0
     

     
     
8007
                           PA4238_tr
                           translation of PA4238
                           333
                           26.12
                           26.42
                           238
                           415.0
     

     
     
200276
                           gb|AAG07626.1|AE004841_4
                           (AE004841) DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa PAO1]
                           333
                           26.12
                           26.42
                           238
                           415.0
     

     
     
200278
                           gb|AAM33636.1|AF506984_1
                           (AF506984) RpoA [Pseudomonas putida]
                           333
                           25.82
                           26.12
                           238
                           409.0
     

     






      

          
GC ORFID: 49618How Found: Glimmer

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: Glimmer Score: 

          
Start: 4182544Stop: 4182257

          
Length: 288


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4238 translation of PA4238Homolog Bit Score 169.0

          
Other Homologs:  t_PA4238 translation of PA4238 (BLASTP 169), psyr_15may02_Scaffold4_revised_gene5212 related to: gi|15599434|ref|NP_252928.1| (NC_002516) DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa] sp|O52760|RPOA_PSEAE DNA-directed RNA polymerase alpha chain (Transcriptase alpha chain) (RNA polymerase alpha subunit) pir||D83113 DNA-dire-TRUNCATED- (BLASTP 164)

          
GC ORF Sequence

           
ATGCAGAGTTCGGTAAATGAGTTCCTGACCCCCCGCCACATCGATGTGCAGGTGGTCAGTCAAACCCGCGCC 
AAGATCACGCTCGAGCCTCTCGAGCGTGGTTTTGGTCACACCCTGGGCAACGCGCTGCGTCGCATCCTGTTG 
TCCTCCATGCCTGGCTGCGCAGTGGTCGAGGCCGAGATCGACGGCGTACTCCACGAGTACTCGGCGATCGAA 
GGTGTGCAGGAAGATGTAATCGAGATCCTGCTGAACCTGAAaaggTCTGGCCATCAAGCTGCACGGTCGTGA