ViewGene
Locus Name:
GeneID:
Location:

GeneID:3691
TrivialName: PA14_42620
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_42620
PAO1 Ortholog Locus:PA1693
Sequence Length:654
Protein Length:217
Start: 3791591
Stop: 3792244
Strand: +
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG05082.1|AE004596_8 (AE004596) translocation protein in type III secretion [Pseudomonas aeruginosa PAO1]
Identities = 217/217 (100%), Positives = 217/217 (100%)
Sequence:
ATGATCCAGTTGCCCGACGAGCTCGGCCTGATCCTCGGCCTGGCCCTGCTCGCGCTGGTCCCGTTCATCGCG
GTGATGGCGACCTCCTTCATCAAGATGACCGTGGTCTTCTCGCTGCTGCGCAACGCCCTGGGCGTCCAGCAG
ATTCCGCCGAACATGGCGATGTACGGGCTGGCGATCATCCTCAGCCTGTACGTGATGGCACCGGTCGGCTTC
GCCACCCGCGATTACCTGCGCAACCACGACGTCAGCCTGAGCGACTCGGCATCGGTGGAACGCTTTCTCGAC
GAGGGCATGGCGCCCTACCGGAACTTCCTCAAGCGGCAGATCCAGGAGCGCGAACACACCTTCTTCATGGAA
AGCACCCGCCAGGTCTGGCCCAGCGAATACGCCGAGCGGCTCGACCCGGACAGCCTGCTGATCCTGCTGCCG
GCCTTCACCGTCAGCGAACTGACCCGTGCGTTCGAGATCGGCTTCCTGATCTACCTGCCCTTCATCGCCATC
GACCTGATCATCTCCAACATCCTCCTGGCGATGGGCATGATGATGGTGTCGCCGATGACCATTTCCCTGCCG
TTCAAGCTGCTCCTGTTCGTCCTCCTCGACGGCTGGGCGCGGCTGACCCACGGCCTGGTCATCAGCTACGGA
GGCTGA
Translation:
MIQLPDELGLILGLALLALVPFIAVMATSFIKMTVVFSLLRNALGVQQIPPNMAMYGLAIILSLYVMAPVGF
ATRDYLRNHDVSLSDSASVERFLDEGMAPYRNFLKRQIQEREHTFFMESTRQVWPSEYAERLDPDSLLILLP
AFTVSELTRAFEIGFLIYLPFIAIDLIISNILLAMGMMMVSPMTISLPFKLLLFVLLDGWARLTHGLVISYG
G*
AnnotationID:3699GeneID:3691
AnnotatorUID: diggins
Modification Date/Time: 2005-02-28 06:06:47
Gene Name:pscR
Confidence Code:2
GeneProduct:translocation protein in type III secretion
Cell Localization:()
Synonyms:yscR
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(19) Protein secretion/export apparatus
Alternate Gene Product Name:
Functional Category Confidence Code:5
COGs:COG4790,pfam00813
Secondary Functional Category(ies):intracellular trafficking and secretion
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAO18040.1| (AY144116) LscR [Photorhabdus luminescens]
          Length = 217

 Score =  362 bits (930), Expect = e-100
 Identities = 179/216 (82%), Positives = 205/216 (94%)

>gb|AAC69787.1| (AF074612) type III secretion protein [Yersinia pestis KIM]
          Length = 217

 Score =  348 bits (893), Expect = 1e-95
 Identities = 173/217 (79%), Positives = 199/217 (91%)

>dbj|BAC59935.1| (AP005078) translocation protein in type III secretion [Vibrio
           parahaemolyticus]
          Length = 216

 Score =  340 bits (871), Expect = 5e-93
 Identities = 165/216 (76%), Positives = 193/216 (89%)






 
Structural Features:
COG4790, EscR, Type III secretory pathway, component EscR 
[Intracellular trafficking and secretion]
CD-Length = 214 residues, 100.0% aligned
Score =  311 bits (798), Expect = 4e-86
Identities = 143/214 (66%), Positives = 180/214 (84%)

pfam00813, FliP, FliP family.
CD-Length = 200 residues,  99.5% aligned
Score =  245 bits (627), Expect = 3e-66
Identities = 114/199 (57%), Positives = 148/199 (74%)






   
Genomic Context:






   
Comment:


















    ReferenceID:7385




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:24527




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:37200




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:3691_cdd.html


    		




 
URL:

















    ReferenceID:37861




  
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:37867




  
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:3691
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
5894
                           PA1693_tr
                           translation of PA1693
                           217
                           99.99
                           99.99
                           0
                           1083.0
     

     
     
165080
                           gb|AAG05082.1|AE004596_8
                           (AE004596) translocation protein in type III secretion [Pseudomonas aeruginosa PAO1]
                           217
                           99.99
                           99.99
                           0
                           1083.0
     

     
     
165081
                           emb|CAD56764.1|
                           (AJ516008) ascR protein [Aeromonas salmonicida subsp. salmonicida]
                           217
                           86.63
                           96.77
                           0
                           966.0
     

     
     
165082
                           emb|CAE16143.1|
                           (BX571871) Type III secretion component protein SctR [Photorhabdus luminescens subsp. laumondii TTO1]
                           217
                           82.94
                           94.47
                           0
                           934.0
     

     
     
165083
                           gb|AAO18040.1|
                           (AY144116) LscR [Photorhabdus luminescens]
                           217
                           82.48
                           94.47
                           0
                           929.0
     

     






      

          
GC ORFID: 46693How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA1693Glimmer Score: 

          
Start: 1162318Stop: 1161665

          
Length: 654


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA1693 translation of PA1693Homolog Bit Score 421.0

          
Other Homologs:  psyr_15may02_Scaffold3_revised_gene4885 (ORF: BLASTX 204.0), psyr_15may02_Scaffold8_revised_gene7931 (ORF: BLASTX 162.0), t_PA1693 (ORF: GLIMMER)

          
GC ORF Sequence

           
ATGATCCAGTTGCCCGACGAGCTCGGCCTGATCCTCGGCCTGGCCCTGCTCGCGCTGGTCCCGTTCATCGCG 
GTGATGGCGACCTCCTTCATCAAGATGACCGTGGTCTTCTCGCTGCTGCGCAACGCCCTGGGCGTCCAGCAG 
ATTCCGCCGAACATGGCGATGTACGGGCTGGCGATCATCCTCAGCCTGTACGTGATGGCACCGGTCGGCTTC 
GCCACCCGCGATTACCTGCGCAACCACGACGTCAGCCTGAGCGACTCGGCATCGGTGGAACGCTTTCTCGAC 
GAGGGCATGGCGCCCTACCGGAACTTCCTCAAGCGGCAGATCCAGGAGCGCGAACACACCTTCTTCATGGAA 
AGCACCCGCCAGGTCTGGCCCAGCGAATACGCCGAGCGGCTCGACCCGGACAGCCTGCTGATCCTGCTGCCG 
GCCTTCACCGTCAGCGAACTGACCCGTGCGTTCGAGATCGGCTTCCTGATCTACCTGCCCTTCATCGCCATC 
GACCTGATCATCTCCAACATCCTCCTGGCGATGGGCATGATGATGGTGTCGCCGATGACCATTTCCCTGCCG 
TTCAAGCTGCTCCTGTTCGTCCTCCTCGACGGCTGGGCGCGGCTGACCCACGGCCTGGTCATCAGCTACGGA 
GGCTGA