ViewGene
Locus Name:
GeneID:
Location:

GeneID:6615
TrivialName: PA14_09120
AnnotatorUID: danlee
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_09120
PAO1 Ortholog Locus:
Sequence Length:711
Protein Length:236
Start: 771686
Stop: 772396
Strand: +
Type:
ChromosomeID:2
Status: INACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Inactivated and Replaced by GeneID 7355. Homology: gb|AAG07626.1|AE004841_4 (AE004841) DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa PAO1]
Identities = 235/236 (99%), Positives = 236/236 (100%)
Sequence:
GTGACGCTGACCCTGGCTAAGAaGGGCTCGGGTGTTGTGACTGCTGCCGATATTCAGCTGGATCACGATGTT
GAGATCATCAACGGTGACCACGTTATCGCCAACCTGGCAGACAACGGCGCGCTGAACATGAAGCTGAAGGTA
GCTCGTGGCCGTGGCTACGAGCCTGCCGATGCACGTCAGAGCGACGAAGACGAAAGCCGCAGCATCGGCCGT
CTGCAGCTCGACGCATCGTTCAGCCCGGTCCGTCGTGTCTCCTACGTGGTGGAAAACGCCCGTGTCGAGCAG
CGCACCAACCTGGACAAACTGGTCCTGGACCTGGAAACCAACGGCACTCTGGATCCCGAAGAGGCTATCCGT
CGCGCCGCTACCATCCTGCAACAGCAGCTGGCAGCGTTCGTGGACCTCAAGGGCGACAGCGAACCCGTCGTT
GAAGAGCAGGAAGACGAGATCGATCCGATCCTCCTGCGCCCGGTCGATGACCTGGAACTGACCGTACGTTCG
GCCAACTGCCTGAAGGCGGAAAACATCTACTACATCGGTGACCTGATCCAGCGCACCGAAGTGGAGCTGTTG
AAAACGCCGAACCTGGGCAAGAAGTCCCTGACCGAAATCAAGGACGTTCTGGCTTCCCGTGGTTTGTCCCTC
GGTATGCGCCTCGATAACTGGCCGCCGGCAAGTCTTAAGAAAGACGACAAGGCCACTGCCTGA
Translation:
MTLTLAKKGSGVVTAADIQLDHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGR
LQLDASFSPVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVV
EEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL
GMRLDNWPPASLKKDDKATA*
AnnotationID:6616GeneID:6615
AnnotatorUID: danlee
Modification Date/Time: 2006-02-01 18:06:42
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:COG0202,pfam03118
Secondary Functional Category(ies):
EC Number:2.7.7.6
Status:INACTIVE
Pathway:






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

 Score =  438 bits (1127), Expect = e-122
 Identities = 224/236 (94%), Positives = 232/236 (98%)

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

 Score =  436 bits (1122), Expect = e-122
 Identities = 223/236 (94%), Positives = 231/236 (97%)

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

 Score =  325 bits (832), Expect = 2e-88
 Identities = 165/226 (73%), Positives = 191/226 (84%)








 
Structural Features:
COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
CD-Length = 317 residues, only  70.0% aligned
Score =  232 bits (593), Expect = 3e-62
Identities = 114/225 (50%), Positives = 152/225 (67%), Gaps = 4/225 (1%)

pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C terminal domain.
CD-Length = 67 residues, 100.0% aligned
Score = 80.6 bits (199), Expect = 1e-16
Identities = 32/67 (47%), Positives = 47/67 (70%)






   
Genomic Context:






   
Comment:


















    ReferenceID:16376




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:30327




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36625




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:6615_cdd.html


    		




 
URL:

















    ReferenceID:36700




  
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:36703




  
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.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6379605









           
Homologs By Global Alignment 

           

       



     
Gene ID:6615
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
8006
                           PA4238_tr
                           translation of PA4238
                           333
                           70.87
                           70.87
                           97
                           1173.0
     

     
     
200170
                           gb|AAG07626.1|AE004841_4
                           (AE004841) DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa PAO1]
                           333
                           70.87
                           70.87
                           97
                           1173.0
     

     
     
200172
                           gb|AAN66109.1|AE016239_4
                           (AE016775) DNA-directed RNA polymerase, alpha subunit [Pseudomonas putida KT2440]
                           333
                           67.56
                           69.66
                           97
                           1130.0
     

     
     
200173
                           gb|AAM33636.1|AF506984_1
                           (AF506984) RpoA [Pseudomonas putida]
                           333
                           67.56
                           69.66
                           97
                           1129.0
     

     
     
200174
                           gb|AAO54193.1|
                           (AE016858) DNA-directed RNA polymerase, alpha subunit [Pseudomonas syringae pv. tomato str. DC3000]
                           333
                           67.26
                           69.36
                           97
                           1125.0
     

     






      

          
GC ORFID: 49617How Found: Glimmer

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: Glimmer Score: 

          
Start: 4182252Stop: 4181542

          
Length: 711


          
Start Codon: GTGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4238 translation of PA4238Homolog Bit Score 456.0

          
Other Homologs:  t_PA4238 translation of PA4238 (BLASTP 456), 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 437)

          
GC ORF Sequence

           
GTGACGCTGACCCTGGCTAAGAaGGGCTCGGGTGTTGTGACTGCTGCCGATATTCAGCTGGATCACGATGTT 
GAGATCATCAACGGTGACCACGTTATCGCCAACCTGGCAGACAACGGCGCGCTGAACATGAAGCTGAAGGTA 
GCTCGTGGCCGTGGCTACGAGCCTGCCGATGCACGTCAGAGCGACGAAGACGAAAGCCGCAGCATCGGCCGT 
CTGCAGCTCGACGCATCGTTCAGCCCGGTCCGTCGTGTCTCCTACGTGGTGGAAAACGCCCGTGTCGAGCAG 
CGCACCAACCTGGACAAACTGGTCCTGGACCTGGAAACCAACGGCACTCTGGATCCCGAAGAGGCTATCCGT 
CGCGCCGCTACCATCCTGCAACAGCAGCTGGCAGCGTTCGTGGACCTCAAGGGCGACAGCGAACCCGTCGTT 
GAAGAGCAGGAAGACGAGATCGATCCGATCCTCCTGCGCCCGGTCGATGACCTGGAACTGACCGTACGTTCG 
GCCAACTGCCTGAAGGCGGAAAACATCTACTACATCGGTGACCTGATCCAGCGCACCGAAGTGGAGCTGTTG 
AAAACGCCGAACCTGGGCAAGAAGTCCCTGACCGAAATCAAGGACGTTCTGGCTTCCCGTGGTTTGTCCCTC 
GGTATGCGCCTCGATAACTGGCCGCCGGCAAGTCTTAAGAAAGACGACAAGGCCACTGCCTGA