ViewGene
Locus Name:
GeneID:
Location:

GeneID:3299
TrivialName: PA14_45630
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_45630
PAO1 Ortholog Locus:PA1455
Sequence Length:744
Protein Length:247
Start: 4059419
Stop: 4058676
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG04844.1|AE004575_3 (AE004575) sigma factor FliA [Pseudomonas aeruginosa PAO1]
Identities = 247/247 (100%), Positives = 247/247 (100%)
Sequence:
ATGACAGCGGCCTCTGGAGTGCGTATGTATAGCAAGGCGCAAGCGCAGAACTCCCAGGAGCAACTGATCCAG
CGTTACGCACCACTGGTCAAGCGCATCGCCTATCACCTGCTCGGCCGCCTGCCGGCCAGCGTGCAGGTGGAG
GACCTGATGCAGGCCGGCATGATCGGCCTGCTCGAGGCCGCGAAGAAATACGACGCCGGCAAGGGCGCCAGC
TTCGAGACCTATGCCGGCATCCGCATCCGCGGGGCCATGCTCGACGAGGTCCGCAAGGGCGACTGGGCGCCT
CGTTCGGTGCACCGCAACACGCGCATGGTGACCGACGCGATCCGCGCGATCGAGGCGAGAACCGGACGCGAC
GCTAAAGATCACGAAGTTGCTGCCGAACTCCAATTGAGCCTCGAAGATTACTACGGCATCCTCAGCGACACG
CAGGGCAGCCGCCTGTACAGCTTCGACGACCTGTTGCAGGACGGCGAACATGGATTGCCGGAAGACACCAGC
CTCAGTCACAACGAACCGATCCACGGCCTGCTCGACGAACGTTTCCAGGCGGCCCTGGCGGATGCCATCGCC
AAGTTGCCGGAGCGCGAGCGCCTGGTGCTGGCGTTGTATTACGACGAGGAACTCAACCTCAAGGAGATCGGC
GAGGTACTGGGCGTCAGCGAATCGCGGGTCAGCCAGTTGCACAGCCAGTGCGCCGCGCGTTTGCGTGCGCGC
CTGGCCGATTGGCGGTCGGCCTGA
Translation:
MTAASGVRMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGKGAS
FETYAGIRIRGAMLDEVRKGDWAPRSVHRNTRMVTDAIRAIEARTGRDAKDHEVAAELQLSLEDYYGILSDT
QGSRLYSFDDLLQDGEHGLPEDTSLSHNEPIHGLLDERFQAALADAIAKLPERERLVLALYYDEELNLKEIG
EVLGVSESRVSQLHSQCAARLRARLADWRSA*
AnnotationID:3307GeneID:3299
AnnotatorUID: diggins
Modification Date/Time: 2005-02-24 12:12:29
Gene Name:fliA
Confidence Code:1
GeneProduct:motility sigma factor FliA
Cell Localization:()
Synonyms:rpoF
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(25) Transcriptional regulators
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG1191
Secondary Functional Category(ies):
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN69920.1|AE016630_11 (AE016790) flagellar biosynthesis sigma factor FliA [Pseudomonas
           putida KT2440]
          Length = 246

 Score =  393 bits (1009), Expect = e-109
 Identities = 202/244 (82%), Positives = 223/244 (91%), Gaps = 2/244 (0%)

>gb|AAO55497.1| (AE016862) motility sigma factor FliA [Pseudomonas syringae pv.
           tomato str. DC3000]
          Length = 246

 Score =  392 bits (1006), Expect = e-108
 Identities = 204/244 (83%), Positives = 221/244 (90%), Gaps = 2/244 (0%)

>dbj|BAC60495.1| (AP005080) flagellar-specific RNA polymerase sigma factor FliA
           [Vibrio parahaemolyticus]
          Length = 244

 Score =  265 bits (677), Expect = 2e-70
 Identities = 138/228 (60%), Positives = 168/228 (73%), Gaps = 1/228 (0%)






 
Structural Features:
COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]
CD-Length = 247 residues,  97.2% aligned
Score =  218 bits (556), Expect = 5e-58
Identities = 99/246 (40%), Positives = 135/246 (54%), Gaps = 8/246 (3%)






   
Genomic Context:






   
Comment:


















    ReferenceID:6601




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:23743




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37365




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3299_cdd.html


    		




 
URL:

















    ReferenceID:37963




  
Author/Investigator(s):
        Starnbach MN, Lory S.





  
Title:
        The fliA (rpoF) gene of Pseudomonas aeruginosa encodes an alternative sigma factor required for flagellin synthesis.




  
PubMed:
        1560774


MedLine:
        




    
Source:
Mol Microbiol. 1992 Feb;6(4):459-69.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=1560774

















    ReferenceID:37964




  
Author/Investigator(s):
        Farinha MA, Ronald SL, Kropinski AM, Paranchych W.





  
Title:
        Localization of the virulence-associated genes pilA, pilR, rpoN, fliA, fliC, ent, and fbp on the physical map of Pseudomonas aeruginosa PAO1 by pulsed-field electrophoresis.




  
PubMed:
        8454366


MedLine:
        




    
Source:
Infect Immun. 1993 Apr;61(4):1571-5.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8454366









           
Homologs By Global Alignment 

           

       



     
Gene ID:3299
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
5295
                           PA1455_tr
                           translation of PA1455
                           247
                           99.99
                           99.99
                           0
                           1242.0
     

     
     
148325
                           gb|AAG04844.1|AE004575_3
                           (AE004575) sigma factor FliA [Pseudomonas aeruginosa PAO1]
                           247
                           99.99
                           99.99
                           0
                           1242.0
     

     
     
148326
                           emb|CAA43548.1|
                           (X61231) sigma-28 class sigma factor [Pseudomonas aeruginosa]
                           247
                           99.99
                           99.99
                           0
                           1242.0
     

     
     
148329
                           gb|AAO55497.1|
                           (AE016862) motility sigma factor FliA [Pseudomonas syringae pv. tomato str. DC3000]
                           248
                           83.06
                           89.91
                           3
                           1009.0
     

     
     
148330
                           gb|AAN03367.1|AF481091_4
                           (AF481091) FliA [Pseudomonas fluorescens]
                           248
                           82.25
                           90.32
                           3
                           1008.0
     

     






      

          
GC ORFID: 46301How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1455Glimmer Score: 

          
Start: 894490Stop: 895233

          
Length: 744


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1455 translation of PA1455Homolog Bit Score 483.0

          
Other Homologs:  psyr_15may02_Scaffold8_revised_gene7939 (ORF: BLASTX 392.0), t_PA1455 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGACAGCGGCCTCTGGAGTGCGTATGTATAGCAAGGCGCAAGCGCAGAACTCCCAGGAGCAACTGATCCAG 
CGTTACGCACCACTGGTCAAGCGCATCGCCTATCACCTGCTCGGCCGCCTGCCGGCCAGCGTGCAGGTGGAG 
GACCTGATGCAGGCCGGCATGATCGGCCTGCTCGAGGCCGCGAAGAAATACGACGCCGGCAAGGGCGCCAGC 
TTCGAGACCTATGCCGGCATCCGCATCCGCGGGGCCATGCTCGACGAGGTCCGCAAGGGCGACTGGGCGCCT 
CGTTCGGTGCACCGCAACACGCGCATGGTGACCGACGCGATCCGCGCGATCGAGGCGAGAACCGGACGCGAC 
GCTAAAGATCACGAAGTTGCTGCCGAACTCCAATTGAGCCTCGAAGATTACTACGGCATCCTCAGCGACACG 
CAGGGCAGCCGCCTGTACAGCTTCGACGACCTGTTGCAGGACGGCGAACATGGATTGCCGGAAGACACCAGC 
CTCAGTCACAACGAACCGATCCACGGCCTGCTCGACGAACGTTTCCAGGCGGCCCTGGCGGATGCCATCGCC 
AAGTTGCCGGAGCGCGAGCGCCTGGTGCTGGCGTTGTATTACGACGAGGAACTCAACCTCAAGGAGATCGGC 
GAGGTACTGGGCGTCAGCGAATCGCGGGTCAGCCAGTTGCACAGCCAGTGCGCCGCGCGTTTGCGTGCGCGC 
CTGGCCGATTGGCGGTCGGCCTGA