ViewGene
Locus Name:
GeneID:
Location:

GeneID:1379
TrivialName: PA14_69190
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_69190
PAO1 Ortholog Locus:PA5239
Sequence Length:1260
Protein Length:419
Start: 6172337
Stop: 6171078
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08624.1|AE004936_7 (AE004936) transcription termination factor Rho [Pseudomonas aeruginosa PAO1]
Identities = 419/419 (100%), Positives = 419/419 (100%)
Sequence:
ATGAATCTGACCGAACTCAAGCAAAAGCCGATTGCCGAACTGCTGGAAATGTCCGATGCCATGGGCCTGGAA
AACATGGCCCGTTCGCGCAAGCAGGACATCATCTTCGCCCTGCTGAAGAAGCACGCGAAAAGTGGTGAAGAG
ATCTCCGGCGATGGCGTGCTGGAGATTCTTCAGGACGGCTTCGGCTTCCTGCGCTCCGCCGACTCTTCCTAC
CTGGCCGGCCCCGACGACATCTATGTCTCGCCGAGCCAGATCCGGCGCTTCAACCTGCGCACGGGCGACACC
ATCATCGGCAAGATCCGGCCGCCGAAAGAGGGCGAACGCTACTTCGCCCTGCTCAAGGTCGACTCGATCAAC
TTCGATCGTCCGGAGAATGCGAAGAACAAGATTCTCTTCGAGAACCTGACGCCGCTGTTCCCCAACGAGCGG
ATGAAGATGGAAGCCGGCAACGGCTCCACCGAAGACCTGACCGGCCGCGTCATCGACCTCTGCGCGCCGATC
GGCAAGGGCCAGCGCGGCCTGATCGTGGCGCCGCCGAAGGCGGGCAAGACCATCATGCTGCAGAACATCGCC
AGCAACATCACCCGCAACAACCCCGAATGCCACCTGATCGTCCTGCTGATCGACGAGCGCCCTGAGGAAGTG
ACCGAAATGCAGCGCACCGTGCGCGGCGAAGTGGTCGCCTCGACCTTTGACGAACCGCCGACCCGTCACGTA
CAGGTCGCCGAGATGGTGATCGAGAAGGCCAAGCGCCTGGTCGAGCACAAGAAGGACGTGGTCATCCTGCTC
GACTCCATCACCCGTCTGGCGCGGGCCTACAACACCGTGATCCCCAGCTCCGGCAAGGTGCTCACCGGCGGT
GTCGACGCCCATGCCCTGGAGAAGCCGAAGCGCTTCTTCGGCGCCGCGCGGAACATCGAAGAGGGCGGTTCT
CTTACGATTCTCGCCACGGCGTTGGTGGAAACCGGCTCGAAGATGGACGAGGTGATCTACGAGGAATTCAAG
GGTACCGGCAACATGGAACTCCCATTGGATCGCAAGATCGCCGAGAAGCGCGTGTTCCCGGCCATCAACATC
AACCGTTCGGGTACCCGCCGCGAAGAGCTGCTGACCAGCGAGGACGAGCTCCAGCGCATGTGGATCCTGCGC
AAGATCCTGCACCCGATGGACGAGATCTCCGCGATCGAATTCCTCATCGACAAGCTCAAGCAGACCAAGACC
AACGATGAGTTCTTCGATTCGATGAAACGGAAGTAG
Translation:
MNLTELKQKPIAELLEMSDAMGLENMARSRKQDIIFALLKKHAKSGEEISGDGVLEILQDGFGFLRSADSSY
LAGPDDIYVSPSQIRRFNLRTGDTIIGKIRPPKEGERYFALLKVDSINFDRPENAKNKILFENLTPLFPNER
MKMEAGNGSTEDLTGRVIDLCAPIGKGQRGLIVAPPKAGKTIMLQNIASNITRNNPECHLIVLLIDERPEEV
TEMQRTVRGEVVASTFDEPPTRHVQVAEMVIEKAKRLVEHKKDVVILLDSITRLARAYNTVIPSSGKVLTGG
VDAHALEKPKRFFGAARNIEEGGSLTILATALVETGSKMDEVIYEEFKGTGNMELPLDRKIAEKRVFPAINI
NRSGTRREELLTSEDELQRMWILRKILHPMDEISAIEFLIDKLKQTKTNDEFFDSMKRK*
AnnotationID:1388GeneID:1379
AnnotatorUID: diggins
Modification Date/Time: 2005-03-16 06:06:56
Gene Name:rho
Confidence Code:2
GeneProduct:transcription termination factor Rho
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:COG1158,cd01128
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70779.1|AE016721_12 (AE016793) transcription termination factor Rho [Pseudomonas putida
           KT2440]
          Length = 419

 Score =  793 bits (2049), Expect = 0.0
 Identities = 398/419 (94%), Positives = 416/419 (99%)

>gb|AAO58668.1| (AE016875) transcription termination factor Rho [Pseudomonas
           syringae pv. tomato str. DC3000]
          Length = 419

 Score =  785 bits (2026), Expect = 0.0
 Identities = 396/419 (94%), Positives = 412/419 (98%)

>gb|AAO09434.1|AE016800_39 (AE016800) Transcription termination factor Rho [Vibrio vulnificus
           CMCP6]
          Length = 419

 Score =  698 bits (1801), Expect = 0.0
 Identities = 347/419 (82%), Positives = 390/419 (93%)






 
Structural Features:
COG1158, Rho, Transcription termination factor [Transcription]
CD-Length = 422 residues,  99.1% aligned
Score =  736 bits (1902), Expect = 0.0
Identities = 334/419 (79%), Positives = 385/419 (91%), Gaps = 1/419 (0%)

cd01128, rho_factor, Transcription termination factor rho is a bacterial 
ATP-dependent RNA/DNA helicase.
CD-Length = 249 residues, 100.0% aligned
Score =  440 bits (1134), Expect = 1e-124







   
Genomic Context:






   
Comment:


















    ReferenceID:2761




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:19906




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:34839




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:1379_cdd.html


    		




 
URL:

















    ReferenceID:35749




  
Author/Investigator(s):
        Miloso M, Limauro D, Alifano P, Rivellini F, Lavitola A, Gulletta E, Bruni CB.





  
Title:
        Characterization of the rho genes of Neisseria gonorrhoeae and Salmonella typhimurium.




  
PubMed:
        8253691


MedLine:
        




    
Source:
J Bacteriol. 1993 Dec;175(24):8030-7.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8253691

















    ReferenceID:35750




  
Author/Investigator(s):
        Pinkham JL, Platt T.





  
Title:
        The nucleotide sequence of the rho gene of E. coli K-12.




  
PubMed:
        6304634


MedLine:
        




    
Source:
Nucleic Acids Res. 1983 Jun 11;11(11):3531-45.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=6304634









           
Homologs By Global Alignment 

           

       



     
Gene ID:1379
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
2517
                           PA5239_tr
                           translation of PA5239
                           419
                           99.99
                           99.99
                           0
                           2115.0
     

     
     
79690
                           gb|AAG08624.1|AE004936_7
                           (AE004936) transcription termination factor Rho [Pseudomonas aeruginosa PAO1]
                           419
                           99.99
                           99.99
                           0
                           2115.0
     

     
     
79691
                           gb|AAN70779.1|AE016721_12
                           (AE016793) transcription termination factor Rho [Pseudomonas putida KT2440]
                           419
                           94.98
                           99.28
                           0
                           2049.0
     

     
     
79692
                           gb|AAO58668.1|
                           (AE016875) transcription termination factor Rho [Pseudomonas syringae pv. tomato str. DC3000]
                           419
                           94.51
                           98.32
                           0
                           2026.0
     

     
     
79693
                           gb|AAA59209.1|
                           (L27278) 'The first ATG in the open reading frame was chosen as the initiation codon.' [Pseudomonas fluorescens]
                           419
                           93.55
                           98.09
                           0
                           2013.0
     

     






      

          
GC ORFID: 44381How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA5239Glimmer Score: 

          
Start: 5436024Stop: 5434765

          
Length: 1260


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TAGTruncated Stop: 

          
Homolog: t_PA5239 translation of PA5239Homolog Bit Score 819.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3211 (ORF: BLASTX 785.0), t_PA5239 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAATCTGACCGAACTCAAGCAAAAGCCGATTGCCGAACTGCTGGAAATGTCCGATGCCATGGGCCTGGAA 
AACATGGCCCGTTCGCGCAAGCAGGACATCATCTTCGCCCTGCTGAAGAAGCACGCGAAAAGTGGTGAAGAG 
ATCTCCGGCGATGGCGTGCTGGAGATTCTTCAGGACGGCTTCGGCTTCCTGCGCTCCGCCGACTCTTCCTAC 
CTGGCCGGCCCCGACGACATCTATGTCTCGCCGAGCCAGATCCGGCGCTTCAACCTGCGCACGGGCGACACC 
ATCATCGGCAAGATCCGGCCGCCGAAAGAGGGCGAACGCTACTTCGCCCTGCTCAAGGTCGACTCGATCAAC 
TTCGATCGTCCGGAGAATGCGAAGAACAAGATTCTCTTCGAGAACCTGACGCCGCTGTTCCCCAACGAGCGG 
ATGAAGATGGAAGCCGGCAACGGCTCCACCGAAGACCTGACCGGCCGCGTCATCGACCTCTGCGCGCCGATC 
GGCAAGGGCCAGCGCGGCCTGATCGTGGCGCCGCCGAAGGCGGGCAAGACCATCATGCTGCAGAACATCGCC 
AGCAACATCACCCGCAACAACCCCGAATGCCACCTGATCGTCCTGCTGATCGACGAGCGCCCTGAGGAAGTG 
ACCGAAATGCAGCGCACCGTGCGCGGCGAAGTGGTCGCCTCGACCTTTGACGAACCGCCGACCCGTCACGTA 
CAGGTCGCCGAGATGGTGATCGAGAAGGCCAAGCGCCTGGTCGAGCACAAGAAGGACGTGGTCATCCTGCTC 
GACTCCATCACCCGTCTGGCGCGGGCCTACAACACCGTGATCCCCAGCTCCGGCAAGGTGCTCACCGGCGGT 
GTCGACGCCCATGCCCTGGAGAAGCCGAAGCGCTTCTTCGGCGCCGCGCGGAACATCGAAGAGGGCGGTTCT 
CTTACGATTCTCGCCACGGCGTTGGTGGAAACCGGCTCGAAGATGGACGAGGTGATCTACGAGGAATTCAAG 
GGTACCGGCAACATGGAACTCCCATTGGATCGCAAGATCGCCGAGAAGCGCGTGTTCCCGGCCATCAACATC 
AACCGTTCGGGTACCCGCCGCGAAGAGCTGCTGACCAGCGAGGACGAGCTCCAGCGCATGTGGATCCTGCGC 
AAGATCCTGCACCCGATGGACGAGATCTCCGCGATCGAATTCCTCATCGACAAGCTCAAGCAGACCAAGACC 
AACGATGAGTTCTTCGATTCGATGAAACGGAAGTAG