ViewGene
Locus Name:
GeneID:
Location:

GeneID:5270
TrivialName: PA14_70450
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_70450
PAO1 Ortholog Locus:PA5337
Sequence Length:267
Protein Length:88
Start: 6278818
Stop: 6279084
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08722.1|AE004946_6 (AE004946) RNA polymerase omega subunit [Pseudomonas aeruginosa PAO1]
Identities = 88/88 (100%), Positives = 88/88 (100%)
Sequence:
ATGGCCCGCGTCACCGTTGAAGACTGCCTGGACAACGTCGATAACCGTTTCGAGCTGGTCATGCTCGCCACC
AAGCGCGCCCGTCAGCTGGCTACCGGCGGCAAGGAGCCGAAAGTGGCCTGGGAAAACGACAAGCCGACCGTC
GTCGCCCTGCGCGAGATCGCTTCCGGCCTGGTCGATGAGAACGTCGTCCAGCAGGAAGACATCGTCGAGGAC
GAACCGCTGTTCGCAGCGTTCGACGACGAGGCCAACACCGAGGCCCTGTAA
Translation:
MARVTVEDCLDNVDNRFELVMLATKRARQLATGGKEPKVAWENDKPTVVALREIASGLVDENVVQQEDIVED
EPLFAAFDDEANTEAL*
AnnotationID:5275GeneID:5270
AnnotatorUID: diggins
Modification Date/Time: 2005-04-26 19:07:20
Gene Name:rpoZ
Confidence Code:2
GeneProduct:RNA polymerase omega subunit
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(24) Transcription, RNA processing and degradation
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1758,pfam01192
Secondary Functional Category(ies):
EC Number:2.7.7.6
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO53628.1| (AE016856) DNA-directed RNA polymerase, omega subunit
          [Pseudomonas syringae pv. tomato str. DC3000]
          Length = 87

 Score =  142 bits (359), Expect = 3e-34
 Identities = 68/84 (80%), Positives = 80/84 (95%)

>gb|AAN70866.1|AE016731_1 (AE016794) DNA-directed RNA polymerase, omega subunit
          [Pseudomonas putida KT2440]
          Length = 87

 Score =  134 bits (338), Expect = 8e-32
 Identities = 64/84 (76%), Positives = 75/84 (89%)

>gb|AAO09354.1|AE016799_252 (AE016799) DNA-directed RNA polymerase, subunit K/omega [Vibrio
          vulnificus CMCP6]
          Length = 90

 Score = 83.2 bits (204), Expect = 3e-16
 Identities = 41/78 (52%), Positives = 56/78 (71%)








 
Structural Features:
COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega [Transcription]
CD-Length = 74 residues, 100.0% aligned
Score = 71.5 bits (175), Expect = 2e-14
Identities = 37/74 (50%), Positives = 48/74 (64%), Gaps = 1/74 (1%)

pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6. 
CD-Length = 55 residues,  96.4% aligned
Score = 54.9 bits (132), Expect = 2e-09
Identities = 28/53 (52%), Positives = 36/53 (67%), Gaps = 1/53 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:10540




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27686




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34770




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5270_cdd.html


    		




 
URL:

















    ReferenceID:35691




  
Author/Investigator(s):
        Gentry DR, Burgess RR.





  
Title:
        The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase.




  
PubMed:
        3549461


MedLine:
        




    
Source:
Gene. 1986;48(1):33-40.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=3549461









           
Homologs By Global Alignment 

           

       



     
Gene ID:5270
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7673
                           PA5337_tr
                           translation of PA5337
                           88
                           99.99
                           99.99
                           0
                           443.0
     

     
     
195460
                           gb|AAG08722.1|AE004946_6
                           (AE004946) RNA polymerase omega subunit [Pseudomonas aeruginosa PAO1]
                           88
                           99.99
                           99.99
                           0
                           443.0
     

     
     
195461
                           gb|AAO53628.1|
                           (AE016856) DNA-directed RNA polymerase, omega subunit [Pseudomonas syringae pv. tomato str. DC3000]
                           88
                           79.54
                           94.31
                           1
                           359.0
     

     
     
195462
                           gb|AAN70866.1|AE016731_1
                           (AE016794) DNA-directed RNA polymerase, omega subunit [Pseudomonas putida KT2440]
                           88
                           75.00
                           88.63
                           1
                           340.0
     

     






      

          
GC ORFID: 48272How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5337Glimmer Score: 

          
Start: 5542507Stop: 5542773

          
Length: 267


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAATruncated Stop: 

          
Homolog: t_PA5337 translation of PA5337Homolog Bit Score 175.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3941 (ORF: BLASTX 142.0), t_PA5337 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGGCCCGCGTCACCGTTGAAGACTGCCTGGACAACGTCGATAACCGTTTCGAGCTGGTCATGCTCGCCACC 
AAGCGCGCCCGTCAGCTGGCTACCGGCGGCAAGGAGCCGAAAGTGGCCTGGGAAAACGACAAGCCGACCGTC 
GTCGCCCTGCGCGAGATCGCTTCCGGCCTGGTCGATGAGAACGTCGTCCAGCAGGAAGACATCGTCGAGGAC 
GAACCGCTGTTCGCAGCGTTCGACGACGAGGCCAACACCGAGGCCCTGTAA