ViewGene
Locus Name:
GeneID:
Location:

GeneID:5316
TrivialName: PA14_65310
AnnotatorUID:
Modification Date/Time:2006-04-06 13:01:23
LocusName:PA14_65310
PAO1 Ortholog Locus:PA4944
Sequence Length:249
Protein Length:82
Start: 5820035
Stop: 5819787
Strand: -
Type:
ChromosomeID:2
Status: ACTIVE
Frame Discrepancy: FALSE
Missense Discrepancy:FALSE
Comments:
Homology: gb|AAG08329.1|AE004907_7 (AE004907) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
Identities = 82/82 (100%), Positives = 82/82 (100%)
Sequence:
ATGTCAAAAGGGCATTCGCTACAAGACCCTTACCTCAATACCCTGCGGAAAGAACGCGTCCCGGTTTCCATC
TATCTGGTCAACGGCATCAAGCTGCAAGGCCAGATCGAGTCCTTCGACCAGTTTGTCATCCTGCTGAAGAAC
ACCGTCAGCCAGATGGTTTACAAGCACGCGATCTCCACCGTGGTACCGAGCCGTCCGGTGCGTCTGCCGAGC
GGTGACCAGCCGGCCGAGCCGGGCAACGCTTGA
Translation:
MSKGHSLQDPYLNTLRKERVPVSIYLVNGIKLQGQIESFDQFVILLKNTVSQMVYKHAISTVVPSRPVRLPS
GDQPAEPGNA*
AnnotationID:5321GeneID:5316
AnnotatorUID: diggins
Modification Date/Time: 2005-03-13 14:02:02
Gene Name:hfq
Confidence Code:2
GeneProduct:putative host factor-I protein
Cell Localization:()
Synonyms:
Cell Localization Confidence Code:5
MolecularFunction:
Functional Category:(22) Related to phage, transposon, or plasmid
Alternate Gene Product Name:putative RNA-binding regulatory protein
Functional Category Confidence Code:5
COGs:COG1923
Secondary Functional Category(ies):transcriptional regulator
EC Number:
Status:ACTIVE
Pathway:






 
Homology:
>gb|AAN70461.1|AE016687_8 (AE016792) host factor-I protein [Pseudomonas putida KT2440]
          Length = 86

 Score =  143 bits (360), Expect = 2e-34
 Identities = 75/88 (85%), Positives = 79/88 (89%), Gaps = 8/88 (9%)

>gb|AAO58370.1| (AE016873) hfq protein [Pseudomonas syringae pv. tomato str.
          DC3000]
          Length = 86

 Score =  139 bits (351), Expect = 3e-33
 Identities = 73/86 (84%), Positives = 75/86 (87%), Gaps = 4/86 (4%)

>gb|AAF93520.1| (AE004123) host factor-I, putative [Vibrio cholerae]
          Length = 87

 Score =  132 bits (333), Expect = 3e-31
 Identities = 65/77 (84%), Positives = 72/77 (93%)






 
Structural Features:
COG1923, Hfq, Uncharacterized host factor I protein
CD-Length = 77 residues, 100.0% aligned
Score =  111 bits (280), Expect = 1e-26
Identities = 52/77 (67%), Positives = 67/77 (87%), Gaps = 1/77 (1%)






   
Genomic Context:






   
Comment:


















    ReferenceID:10632




  
Author/Investigator(s):
        GenNotator





  
Title:
        




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:BLASTP 







    
Data:


    		




 
URL:

















    ReferenceID:27779




  
Author/Investigator(s):
        GenNotator





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:RPSBLAST 







    
Data:


    		




 
URL:

















    ReferenceID:35111




  
Author/Investigator(s):
        





  
Title:
        CDD Search




  
PubMed:
        


MedLine:
        




    
Source:






    
Reference Type:Misc (text/plain)







    
Data:5316_cdd.html


    		




 
URL:

















    ReferenceID:35901




  
Author/Investigator(s):
        Kajitani M, Ishihama A.





  
Title:
        Identification and sequence determination of the host factor gene for bacteriophage Q beta.




  
PubMed:
        2020545


MedLine:
        




    
Source:
Nucleic Acids Res. 1991 Mar 11;19(5):1063-6.






    
Reference Type:Journal 







    
Data:


    		




 
URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=2020545









           
Homologs By Global Alignment 

           

       



     
Gene ID:5316
           
Identity:

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

                           

     
HomologID
                           Accession
                           Description
                           Length
                           PctIdentity
                           PctSimilarity
                           Gaps
                           Score
     

     
     
7716
                           PA4944_tr
                           translation of PA4944
                           82
                           99.99
                           99.99
                           0
                           417.0
     

     
     
195920
                           gb|AAG08329.1|AE004907_7
                           (AE004907) conserved hypothetical protein [Pseudomonas aeruginosa PAO1]
                           82
                           99.99
                           99.99
                           0
                           417.0
     

     
     
195921
                           gb|AAN70461.1|AE016687_8
                           (AE016792) host factor-I protein [Pseudomonas putida KT2440]
                           88
                           85.22
                           89.77
                           8
                           367.0
     

     
     
195922
                           gb|AAO58370.1|
                           (AE016873) hfq protein [Pseudomonas syringae pv. tomato str. DC3000]
                           86
                           84.88
                           87.20
                           4
                           354.0
     

     
     
195943
                           gb|AAA24175.1|
                           (M63655) ORF [Escherichia coli]
                           82
                           79.26
                           82.92
                           3
                           314.0
     

     






      

          
GC ORFID: 48318How Found: BLASTX

          
GC_TrimmedSeqID: 69Blast Result ID

          
Subject Sequence Name: t_PA4944Glimmer Score: 

          
Start: 5083716Stop: 5083468

          
Length: 249


          
Start Codon: ATGTruncated Start:

          
Stop Codon: TGATruncated Stop: 

          
Homolog: t_PA4944 translation of PA4944Homolog Bit Score 165.0

          
Other Homologs:  psyr_15may02_Scaffold2_revised_gene3430 (ORF: BLASTX 139.0)

          
GC ORF Sequence

           
ATGTCAAAAGGGCATTCGCTACAAGACCCTTACCTCAATACCCTGCGGAAAGAACGCGTCCCGGTTTCCATC 
TATCTGGTCAACGGCATCAAGCTGCAAGGCCAGATCGAGTCCTTCGACCAGTTTGTCATCCTGCTGAAGAAC 
ACCGTCAGCCAGATGGTTTACAAGCACGCGATCTCCACCGTGGTACCGAGCCGTCCGGTGCGTCTGCCGAGC 
GGTGACCAGCCGGCCGAGCCGGGCAACGCTTGA