ViewGene
Locus Name:
GeneID:
Location:

GeneID:5300
TrivialName: PA14_42630
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_42630
PAO1 Ortholog Locus:PA1692
Sequence Length:267
Protein Length:88
Start: 3792247
Stop: 3792513
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05081.1|AE004596_7 (AE004596) probable translocation protein in type III secretion [Pseudomonas aeruginosa PAO1]
Identities = 88/88 (100%), Positives = 88/88 (100%)
Sequence:
ATGAGCAGCGCCGACATCCTCCACTTCACCAACCAGACCCTGTGGCTGGTGCTGGTCCTGTCGCTGCCGCCG
GTACTGGTCGCGGCCCTGATCGGCACCCTGGTATCGCTGGTCCAGGCACTCACCCAGATCCAGGAGCAGACC
CTCGGCTTCGTCGCCAAGCTGGTGGCCGTGGTGGTGGTACTGTTCGCCACCAGCGGCTGGCTGGGCGGCGAG
CTGTACCGTTTCGCCGAAATGACCCTGCTGAAGGTGCCGCTGGTGCGATGA
Translation:
MSSADILHFTNQTLWLVLVLSLPPVLVAALIGTLVSLVQALTQIQEQTLGFVAKLVAVVVVLFATSGWLGGE
LYRFAEMTLLKVPLVR*
AnnotationID:5305GeneID:5300
AnnotatorUID: diggins
Modification Date/Time: 2005-02-28 06:06:54
Gene Name:
Confidence Code:3
GeneProduct:putative translocation protein in type III secretion
Cell Localization:()
Synonyms:pscS
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(19) Protein secretion/export apparatus
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG4794
Secondary Functional Category(ies):intracellular trafficking and secretion
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAC69786.1| (AF074612) type III secretion protein [Yersinia pestis KIM]
          Length = 88

 Score =  135 bits (341), Expect = 4e-32
 Identities = 66/88 (75%), Positives = 78/88 (88%)

>gb|AAN37514.1| (AY150843) YscS [Yersinia enterocolitica]
          Length = 88

 Score =  135 bits (341), Expect = 4e-32
 Identities = 66/88 (75%), Positives = 78/88 (88%)

>emb|CAB54922.1| (AL117189) putative type III secretion protein [Yersinia pestis]
          Length = 88

 Score =  135 bits (341), Expect = 4e-32
 Identities = 66/88 (75%), Positives = 78/88 (88%)








 
Structural Features:
COG4794, EscS, Type III secretory pathway, component EscS 
[Intracellular trafficking and secretion]
CD-Length = 89 residues,  98.9% aligned
Score = 91.0 bits (226), Expect = 3e-20
Identities = 52/88 (59%), Positives = 64/88 (72%)






   
Genomic Context:






   
Comment:
other possible gene name: yscR


















    ReferenceID:10600




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27747




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:36514




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5300_cdd.html


    		




 
URL:

















    ReferenceID:37863




  
Author/Investigator(s):
        Bergman T, Erickson K, Galyov E, Persson C, Wolf-Watz H.





  
Title:
        The lcrB (yscN/U) gene cluster of Yersinia pseudotuberculosis is involved in Yop secretion and shows high homology to the spa gene clusters of Shigella flexneri and Salmonella typhimurium.




  
PubMed:
        8169210


MedLine:
        




    
Source:
J Bacteriol. 1994 May;176(9):2619-26.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8169210

















    ReferenceID:37866




  
Author/Investigator(s):
        Fields KA, Plano GV, Straley SC.





  
Title:
        A low-Ca2+ response (LCR) secretion (ysc) locus lies within the lcrB region of the LCR plasmid in Yersinia pestis.




  
PubMed:
        8300512


MedLine:
        




    
Source:
J Bacteriol. 1994 Feb;176(3):569-79.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8300512









           
Homologs By Global Alignment 

           

       



     
Gene ID:5300
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7701
                           PA1692_tr
                           translation of PA1692
                           88
                           99.99
                           99.99
                           0
                           425.0
     

     
     
195825
                           gb|AAG05081.1|AE004596_7
                           (AE004596) probable translocation protein in type III secretion [Pseudomonas aeruginosa PAO1]
                           88
                           99.99
                           99.99
                           0
                           425.0
     

     
     
195826
                           gb|AAO18039.1|
                           (AY144116) LscS [Photorhabdus luminescens]
                           88
                           77.27
                           90.90
                           0
                           355.0
     

     
     
195827
                           emb|CAD56765.1|
                           (AJ516008) ascS protein [Aeromonas salmonicida subsp. salmonicida]
                           88
                           77.27
                           88.63
                           0
                           351.0
     

     
     
195835
                           gb|AAA27679.1|
                           (L25667) yscS [Yersinia pseudotuberculosis]
                           88
                           75.00
                           88.63
                           0
                           341.0
     

     






      

          
GC ORFID: 48302How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1692Glimmer Score: 

          
Start: 1161662Stop: 1161396

          
Length: 267


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1692 translation of PA1692Homolog Bit Score 168.0

          
Other Homologs:  t_PA1692 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGAGCAGCGCCGACATCCTCCACTTCACCAACCAGACCCTGTGGCTGGTGCTGGTCCTGTCGCTGCCGCCG 
GTACTGGTCGCGGCCCTGATCGGCACCCTGGTATCGCTGGTCCAGGCACTCACCCAGATCCAGGAGCAGACC 
CTCGGCTTCGTCGCCAAGCTGGTGGCCGTGGTGGTGGTACTGTTCGCCACCAGCGGCTGGCTGGGCGGCGAG 
CTGTACCGTTTCGCCGAAATGACCCTGCTGAAGGTGCCGCTGGTGCGATGA